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Microbial communities exhibit complex behaviors driven by species interactions and individual characteristics. In this study, we delve into the dynamics of a mixed bacterial population comprising two distinct species with different morphology and motility aspects. Employing agent-based modeling and computer simulations, we analyze the impacts of size ratios and packing fractions on dispersal patterns, aggregate formation, clustering, and spatial ordering. Notably, we find that motility and anisotropy of elongated bacteria significantly influence the distribution and spatial organization of nonmotile spherical species. Passive spherical cells display a superdiffusive behavior, particularly at larger size ratios in the ballistic regime. As the size ratio increases, clustering of passive cells is observed, accompanied by enhanced alignment and closer packing of active cells in the presence of higher passive cell area fractions. In addition, we identify the pivotal role of passive cell area fraction in influencing the response of active cells toward nematicity, with its dependence on size ratio. These findings shed light on the significance of morphology and motility in shaping the collective behavior of microbial communities, providing valuable insights into complex microbial behaviors with implications for ecology, biotechnology, and bioengineering. [ABSTRACT FROM AUTHOR]

Many female squids and cuttlefishes have a symbiotic reproductive organ called the accessory nidamental gland (ANG) that hosts a bacterial consortium involved with egg defense against pathogens and fouling organisms. While the ANG is found in multiple cephalopod families, little is known about the global microbial diversity of these ANG bacterial symbionts. We used 16S rRNA gene community analysis to characterize the ANG microbiome from different cephalopod species and assess the relationship between host and symbiont phylogenies. The ANG microbiome of 11 species of cephalopods from four families (superorder: Decapodiformes) that span seven geographic locations was characterized. Bacteria of class Alphaproteobacteria, Gammaproteobacteria, and Flavobacteriia were found in all species, yet analysis of amplicon sequence variants by multiple distance metrics revealed a significant difference between ANG microbiomes of cephalopod families (weighted/unweighted UniFrac, Bray-Curtis, P = 0.001). Despite being collected from widely disparate geographic locations, members of the family Sepiolidae (bobtail squid) shared many bacterial taxa including (~50%) Opitutae (Verrucomicrobia) and Ruegeria (Alphaproteobacteria) species. Furthermore, we tested for phylosymbiosis and found a positive correlation between host phylogenetic distance and bacterial community dissimilarity (Mantel test r = 0.7). These data suggest that closely related sepiolids select for distinct symbionts from similar bacterial taxa. Overall, the ANGs of different cephalopod species harbor distinct microbiomes and thus offer a diverse symbiont community to explore antimicrobial activity and other functional roles in host fitness.IMPORTANCEMany aquatic organisms recruit microbial symbionts from the environment that provide a variety of functions, including defense from pathogens. Some female cephalopods (squids, bobtail squids, and cuttlefish) have a reproductive organ called the accessory nidamental gland (ANG) that contains a bacterial consortium that protects eggs from pathogens. Despite the wide distribution of these cephalopods, whether they share similar microbiomes is unknown. Here, we studied the microbial diversity of the ANG in 11 species of cephalopods distributed over a broad geographic range and representing 15-120 million years of host divergence. The ANG microbiomes shared some bacterial taxa, but each cephalopod species had unique symbiotic members. Additionally, analysis of host-symbiont phylogenies suggests that the evolutionary histories of the partners have been important in shaping the ANG microbiome. This study advances our knowledge of cephalopod-bacteria relationships and provides a foundation to explore defensive symbionts in other systems.

Aquatic hyphomycetes are key organisms that perform the decomposition of plant organic matter in streams. They are strongly influenced by nitrogen availability and temperature. Both environmental parameters stimulate aquatic hyphomycete activity (litter decomposition and conidia production) while high temperature tends to lower their diversity. However, the past research mostly focused on temperate streams, and tropical studies remain comparatively too scarce to determine if current knowledge applies to tropical aquatic hyphomycetes. Here, we provide the first assessment of aquatic hyphomycete communities and microbial litter decomposition in streams of Guadeloupe, which exhibit naturally warm and oligotrophic conditions. Local gradients of temperature and nitrate concentration allowed to test the hypothesis that microbial litter decomposition is stimulated by nitrate and temperature. To the contrary, we expected the warmer downstream sites to exhibit lower aquatic hyphomycete diversity due to high temperature. Contrary to our expectations, diversity increased along both nitrate and temperature gradients, while decomposition process was stimulated by nitrate but not by temperature. One implication of these findings is that warm water in the tropics is not necessarily associated with low aquatic hyphomycete diversity. Future studies should investigate the effect of temperature using broad and independent gradients of temperature (latitude, altitude and season). [ABSTRACT FROM AUTHOR]

To evaluate the effect of glyphosate, 2,4-D, and their combination on daily dissolved oxygen saturation percentage (DO%) in freshwater, two separate outdoor mesocosm experiments were performed. The experiments were conducted under contrasting conditions: one in clear mesotrophic status lasting 23 days, and the other in organic turbid eutrophic conditions lasting 21 days. Single concentrations were applied as commercial formulations at two levels. Samples of phytoplankton (micro + nano, picoeukaryotes, picocyanobacteria), mixotrophic algae, and heterotrophic bacteria were analyzed at four sampling dates. Increases in DO levels were consistently observed in both clear and turbid systems treated with glyphosate, either alone or in combination with 2,4-D, suggesting that DO is a sensitive indicator. DO increased in all glyphosate treatments. DO increases reflected different changes in phytoplankton communities, increasing with micro + nano phytoplankton abundance in the clear experiment but with increased picocyanobacteria in the turbid. In contrast, 2,4-D reduced DO levels, but only in the turbid system, where micro + nano phytoplankton abundance decreased. The clear system showed greater resilience by restoring DO levels before the turbid one. Mainly additive effects of the herbicide mixture were observed on dissolved oxygen levels (DO%), but a distinct synergistic decrease was detected within turbid systems, underscoring the importance of considering turbidity as a contributing factor in the freshwater impacts of herbicides. [ABSTRACT FROM AUTHOR]

Hatcheries nationwide suffer from unexplained acute production failures, termed crashes. The microbiota of oysters relates to larval health with previous studies showing that some bacterial species have positive and others negative effects on oyster health. To investigate microbial correlates of crashes, we collected samples from every batch of oyster larvae (Crassostrea virginica) produced by the Horn Point Laboratory Oyster Hatchery since 2021 and analyzed the microbiota of 15 of those batches over their duration in the hatchery, from age of 3 to 5 days until either harvest or complete die off of the batch. Across events, die-offs generally became evident at or after six days of age. We found that the microbiota of oyster larvae appears to respond to die-off events with crashed batches having fundamentally different microbiota than good batches at age 7 to 9 and 9 to 12 days. Crashed batches were often taken over by microeukaryotes and bacterial taxa from the Protobacteria and Bacteroidetes phyla. However, this presumably opportunistic community differed between batches. Observed Vibrio species level groups did not appear to be oyster pathogens and appeared to respond to, rather than precede, crashes. The microbiota of 3 to 5 day old larvae were statistically related to whether a die-off occurred later in the larval batches' life, only when the taxa were first agglomerated to family level. The detection of two microbial species not previously known to associate with oysters, along with an increased presence of Dinophyceae, predominantly the toxin-producing Gyrodinium jinhaense, in 3 to 5 day old oyster larvae was statistically linked with subsequent batch crashes. This study suggests that the health of larval oysters shapes their microbiome. Conversely, it provides hints that the microbiome of larvae, and perhaps harmful algae, may drive hatchery crashes. [ABSTRACT FROM AUTHOR]

In microbial community sequencing, involving bacterial ribosomal 16S rDNA or fungal ITS, the targeted genes are the basis for taxonomical assignment. The traditional bioinformatical procedure has for decades made use of a clustering protocol by which sequences are pooled into packages of shared percent identity, typically at 97%, to yield Operational Technical Units (OTUs). Progress in the data processing methods has however led to the possibility of minimizing technical sequencers errors, which were the main reason for the OTU choice, and to analyze instead the exact Amplicon Sequence Variants (ASV) which is a choice yielding much less agglomerated reads. We have tested the two procedures on the same 16S metabarcoded bacterial amplicons dataset encompassing a series of samples from 17 adjacent habitats, taken across a 700 meter-long transect of different ecological conditions unfolding in a gradient spanning from cropland, through meadows, forest and all successional transitions up to the seashore, within the same coastal area. This design allowed to scan a high biodiversity basin and to measure alpha, beta and gamma diversity of the area, to verify the effect of the bioinformatics on the same data as concerns the values of ten different ecological indexes and other parameters. Two levels of progressive OTUs clustering, (99% and 97%) were compared with the ASV data. The results showed that the OTUs clustering proportionally led to a marked underestimation of the ecological indicators values for species diversity and to a distorted behaviour of the dominance and evenness indexes with respect to the direct use of the ASV data. Multivariate ordination analyses resulted also sensitive in terms of tree topology and coherence. Overall, data support the view that reference-based OTU clustering carries several misleading disadvantageous biases, including the risk of missing novel taxa which are yet unreferenced in databases. Since its alternatives as de novo clustering have on the other hand drawbacks due to heavier computational demand and results comparability, especially for environmental studies which contain several yet uncharacterized species, the direct ASV based analysis, at least for prokaryotes, appears to warrant significand advantages in comparison to OTU clustering at every level of percent identity cutoff. [ABSTRACT FROM AUTHOR]

Switchgrass (Panicum virgatum L.) is a native, low-input North American perennial crop primarily grown for bioenergy, livestock forage, and industrial fiber. To achieve no-input switchgrass production that meets biomass needs, several switchgrass genotypes have been identified that have a low or negative response to nitrogen fertilizer, i.e., the biomass accumulation with added nitrogen is less than or equal to that when grown without nitrogen. In order to improve the viability of low-input switchgrass production, a more detailed understanding of the biogeochemical mechanisms active in these select genotypes is needed. 16S and ITS amplicon sequencing and qPCR of key functional genes were applied to switchgrass rhizospheres to elucidate microbial community structure in high-producing, no-input switchgrass families. Rhizosphere microbial community structure differed strongly between sites, and nitrogen responsiveness. [ABSTRACT FROM AUTHOR]

Major theories regarding microbe‐mediated plant community dynamics assume that plant species cultivate distinct microbial communities. However, few studies empirically assess the role of species‐associated microbial community dissimilarity in plant competitive dynamics.In this study, we paired a competition experiment between eight annual forbs with characterisation of species‐associated fungal communities to assess whether mycobiome dissimilarity is associated with pairwise competitive dynamics.Using a quantitative approach informed by modern coexistence theory, we found that fungal dissimilarity was correlated with both increased stabilising niche differences and fitness inequalities. Additionally, we found that the probability of coexistence increased with mycobiome dissimilarity.When subsetting the community into different fungal functional groups (pathotrophs, saprotrophs, symbiotrophs), overall relationships between dissimilarity and competitive dynamics were independent of these functional groups.Synthesis. These results suggest that fungal community divergence may play an important role in mediating plant competitive dynamics. Although fungal community dissimilarity is associated with both niche and fitness differences, complex biotic and/or abiotic interactions below‐ground may result in an observed correlation between fungal community dissimilarity and plant coexistence. Ultimately, this study suggests a novel approach to better understanding how microbiome dissimilarity may impact host community dynamics. [ABSTRACT FROM AUTHOR]

Organic management enhances the formation of distinct and stable soil microbial communities, however, its influence on the temporal recovery of microbiome and multifunctionality of sterilized soil remains poorly understood.We used amplicon sequencing and metagenomic sequencing to investigate the effects of microbial communities in long‐term organic and conventional managed soils on restoring soil microbiome and functionality. We calculated multifunctionality of soils at days 30 and 90 of recolonization using the averaging approach.Results showed that organic management (O) significantly increased alpha diversity, niche width and network complexity of microbial community compared to conventional management (C). The alpha diversity, niche width and network complexity of microbial community in soils with organic soil suspension were significantly increased compared to conventional management at days 30 and 90 of recolonization. Soil multifunctionality of sterilized organic managed soil inoculated with organic soil suspension (OO) was 14.6% to 70.6% higher than that of the rest treatments. Macrogenomic analysis revealed that O significantly enriched functional pathways of ABC transporters, carbon metabolism, biosynthesis of amino acids, two‐component and nitrogen metabolism as well as most of the functional genes for carbon degradation, carbon fixation, nitrogen cycling and phosphorus cycles compared to C. These functional pathways and genes were also significantly enriched in soils with organic soil suspension at day 30 and 90 of recolonization. Furthermore, alpha diversity, niche width, network complexity, functional pathways and functional genes of microbiome correlated positively with soil multifunctionality.Synthesis and applications. Our results emphasize the importance of organic management induced changes in diversity, network complexity, and functionality of microbial communities for promoting recovery to soil microbial and functional losses, providing the theoretical basis for sustainable impact of organic management in agronomic production on soil microbiome and function. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Summary: Daqu is an essential saccharification and fermentation agent in Baijiu brewing, and its characteristics affect the yield, quality, and flavour of Baijiu. The fundamental reason is that Daqu can provide rich microbial resources, complex enzyme systems, and raw materials for the Baijiu brewing process. In this study, three sauce‐flavour Daqu from two production areas, Beijing and Guizhou, were selected to focus on discussing and analysing the main contributions of sauce‐flavour Daqu itself to Baijiu brewing without interference from the external environment. The differences in the flavour composition and microbial communities of three Daqu were analysed. Microbial biomarkers were analysed by Lefse multilevel discriminant analysis for three Daqu. We found that different regions have their own biomarkers. Citrobacter, Rhodococcus, and Pseudomonas, were biomarkers of HD Daqu. Oceanobacillus, Aspergillus and Pichia were biomarkers of MT Daqu. Bacillus, Pediococcus and Fusarium were biomarkers of WM Daqu. A solid‐state simulation fermentation experiment was carried out to analyse changes in the flavour composition and microbial communities of fermented grains after 35 days of fermentation. The results showed that the microbial communities and the flavour composition in the Daqu and fermented samples differed significantly. The dominant microorganism genus evolved from Citrobacter, Rhodococcus, and Thermomyces to Lactobacillus, Pediococcus, and Pichia HD sample. The dominant microorganism genus in WM sample changed from Virgibacillus, Oceanobacillus, and Thermomyces to Lactobacillus, Pediococcus, and Pichia. Whereas in MT sample, the dominant microorganism genus evolved from Virgibacillus, Kroppenstedtia, and Thermomyces to Lactobacillus, Pediococcus, and Pichia. Additionally, the main flavour composition also changed after fermentation, which in the late fermentation period were phenylethyl alcohol, ethyl palmitate, tetramethylpyrazine, and 3‐methylbutanoic acid. These findings can provide support to explain the importance and contribution of sauce‐flavour Daqu in Baijiu brewing scientifically. [ABSTRACT FROM AUTHOR]

In this experiment, alfalfa silage with different packing densities (500 kg/m3、600 kg/m3 and 700 kg/m3) was prepared under the conditions of outdoor high temperature and indoor room temperature, respectively. At the same time, the same lactobacillus additive was used for fermentation in each density treatment group. The chemical composition, fermentation quality and microbial community of alfalfa silage were analyzed. The results showed that the contents of dry matter (DM) and water-soluble carbohydrate (WSC) decreased with the increase of density during fermentation at high temperature. At the same time, when the density is 600 kg/m³, CP (crude protein) content is the highest, ADF (acid detergent fiber) content is the lowest. The contents and pH values of neutral detergent fiber (NDF), lactic acid (LA) and lactic acid bacteria (LAB) were significantly affected by temperature (p < 0.05). Density had significant effects on DM, NDF, WSC and LA contents (p < 0.05). The interaction between temperature and density had significant effects on the content of ADF and LAB (p < 0.05). At the same time, the abundance of Lactiplantibacillus plantarum in high temperature fermented silage was lower than that in normal temperature fermented feed. The number of Lactiplantibacillus plantarum in room temperature treatment group decreased with the increase of density. In summary, this study clarified the effects of different temperature and density on alfalfa fermentation quality and microbial community, and clarified that the density should be reasonably controlled within 600 kg/m³ during alfalfa silage, providing theoretical support for production practice. [ABSTRACT FROM AUTHOR]

ABSTRACT Aim Location Time Period Major Taxa Studied Methods Results Conclusion Ecological theory suggests that dispersal limitation and selection by climatic factors influence bacterial community assembly at a continental scale, yet the conditions governing the relative importance of each process remains unclear. The carnivorous pitcher plant Sarracenia purpurea provides a model aquatic microecosystem to assess bacterial communities across the host plant's north–south range in North America. This study determined the relative influences of dispersal limitation and environmental selection on the assembly of bacterial communities inhabiting S. purpurea pitchers at the continental scale.Eastern United States and Canada.2016.Bacteria inhabiting S. purpurea pitchers.Pitcher morphology, fluid, inquilines and prey were measured, and pitcher fluid underwent DNA sequencing for bacterial community analysis. Null modelling of β‐diversity provided estimates for the contributions of selection and dispersal limitation to community assembly, complemented by an examination of spatial clustering of individuals. Phylogenetic and ecological associations of co‐occurrence network module bacteria was determined by assessing the phylogenetic diversity and habitat preferences of member taxa.Dispersal limitation was evident from between‐site variation and spatial aggregation of individual bacterial taxa in the S. purpurea pitcher system. Selection pressure was weak across the geographic range, yet network module analysis indicated environmental selection within subgroups. A group of aquatic bacteria held traits under selection in warmer, wetter climates, and midge abundance was associated with selection for traits held by a group of saprotrophs. Processes that increased pitcher fluid volume weakened selection in one module, possibly by supporting greater bacterial dispersal.Dispersal limitation governed bacterial community assembly in S. purpurea pitchers at a continental scale (74% of between‐site comparisons) and was significantly greater than selection across the range. Network modules showed evidence for selection, demonstrating that multiple processes acted concurrently in bacterial community assembly at the continental scale. [ABSTRACT FROM AUTHOR]

Increasing plastic pollution is a serious environmental problem as widespread production and inadequate disposal of plastic materials lead to adverse impacts on ecosystems. The structural and functional characteristics of the anaerobic microbial community contacting with extruded polystyrene (XPS) waste were investigated under methanogenic (MG) and nitrate-(NR) and sulfate-reducing (SR) conditions. The presence of XPS in the microbial community was shown to have no negative effect on the processes of biogas formation and, on the contrary, resulted in an increase in the yield of methane and volatile fatty acids and a change in their ratio. Microparticles of different sizes were found in the culture liquid of the variants with XPS: 2.4 × 106/mL (NR), 1.2 × 106/mL (SR), and 0.4 × 106/mL (MG), while no microparticles were found in the control variants. Scanning electron microscopy revealed that in all experimental variants the surface of the polymer became looser, more textured, with formation of irregularities, cracks, and holes. Increased diversity in the microbial community associated with an increase in the number of microbial morphotypes, correlated with the results of high-throughput sequencing of the 16S rRNA gene. When XPS was introduced into an anaerobic community incubated in different donor-acceptor conditions, the number of microbial groups in it increased, as well as the proportion of hydrolytic and acidogenic bacteria (Sedimentibacter, Lentimicrobium), acetogenic syntrophs (Syntrophomonas, Desulfovibrio, Geobacter), and methanogenic archaea (Methanosarcina, Methanobacterium). Our study showed that the XPS waste was not inert for the microbial community, the contact with it resulting in significant changes in its structure and functioning. Changes in the sample surface, emergence of microparticles, and differences in the composition of the intermediate and terminal metabolic products may indicate slow partial degradation of the plastic via fragmentation. However, since the experiments were carried out using household XPS containing various fillers apart from the main polymer, it is probable that, along with polystyrene, additional substances included in its composition (plasticizers, dyes, etc.) are also subject to degradation. The ability of microorganisms to degrade the polymer itself requires further research. [ABSTRACT FROM AUTHOR]

The microbial communities of bottom sediments of the Bolshaya Zelenovskaya oil seepage site (Lake Baikal) were investigated to assess their diversity and potential functional activity in the anaerobic degradation of oil. Microorganisms of the subsurface and deep sediment layers were grown in enrichment cultures supplemented with oil and various electron acceptors for 1 year at 10°C, and it was found that the concentrations of n-alkanes and polyaromatic hydrocarbons decreased by 1.2–2 and 2.2–2.8 times, respectively. Hydrocarbon conversion was accompanied by generation of hydrocarbon gases (methane and ethane). The microbial community of subsurface sediments had a higher bacterial diversity than the community of deep horizons and was composed of microorganisms specialized in degradation of a broad range of substrates, including oil hydrocarbons. The community of the deep sediment layer was dominated by Atribacterota, Caldisericota, and Bathyarchaeia (Thermoproteota), as well as members of the "rare biosphere": Elusimicrobiota and Candidatus Hadarchaeota. Apparently, oil degradation in the bottom sediments of Lake Baikal is primarily mediated by members of the phyla Bacillota, Pseudomonadota, Chloroflexota, Actinomycetota, Desulfobacterota, Atribacterota, Halobacteriota, and Bathyarchaeia (Thermoproteota). [ABSTRACT FROM AUTHOR]

Leaf litter in coastal wetlands lays the foundation for carbon storage, and the creation of coastal wetland soils. As climate change alters the biogeochemical conditions and macrophyte composition of coastal wetlands, a better understanding of the interactions between microbial communities, changing chemistry, and leaf litter is required to understand the dynamics of coastal litter breakdown in changing wetlands. Coastal wetlands are dynamic systems with shifting biogeochemical conditions, with both tidal and seasonal redox fluctuations, and marine subsidies to inland habitats. Here, we investigated gene expression associated with various microbial redox pathways to understand how changing conditions are affecting the benthic microbial communities responsible for litter breakdown in coastal wetlands. We performed a reciprocal transplant of leaf litter from four distinct plant species along freshwater‐to‐marine gradients in the Florida Coastal Everglades, tracking changes in environmental and litter biogeochemistry, as well as benthic microbial gene expression associated with varying redox conditions, carbon degradation, and phosphorus acquisition. Early litter breakdown varied primarily by species, with highest breakdown in coastal species, regardless of the site they were at during breakdown, while microbial gene expression showed a strong seasonal relationship between sulfate cycling and salinity, and was not correlated with breakdown rates. The effect of salinity is likely a combination of direct effects, and indirect effects from associated marine subsidies. We found a positive correlation between sulfate uptake and salinity during January with higher freshwater inputs to coastal areas. However, we found a peak of dissimilatory sulfate reduction at intermediate salinity during April when freshwater inputs to coastal sites are lower. The combination of these two results suggests that sulfate acquisition is limiting to microbes when freshwater inputs are high, but that when marine influence increases and sulfate becomes more available, dissimilatory sulfate reduction becomes a key microbial process. As marine influence in coastal wetlands increases with climate change, our study suggests that sulfate dynamics will become increasingly important to microbial communities colonizing decomposing leaf litter. [ABSTRACT FROM AUTHOR]

A central challenge in community ecology is understanding and predicting the effects of abiotic factors on community assembly. In particular, microbial communities play a central role in the ecosystem, but we do not understand how changing factors like temperature are going to affect community composition or function. In this article, we studied the self-assembly of multiple communities in synthetic environments to understand changes in microbial community composition based on metabolic responses of different functional groups along a temperature gradient. In many microbial communities, different microbial functional groups coexist through the partitioning of carbon sources in an emergent trophic structure (cross-feeding). In this system, respirofermentative bacteria display a preference for the sugars supplied as the only carbon source but secrete secondary carbon sources (organic acids) that are more efficiently consumed by obligate respirators. As a consequence of this trophic structure, the metabolic plasticity of the respirofermenters has downstream consequences for the relative abundance of respirators across temperatures. We found that the effects of different temperatures on microbial composition can largely be described by an increase in fermentation by-products with increasing temperatures from the respirofermentative bacteria. This research highlights the importance of metabolic plasticity and metabolic trade-offs in predicting species interactions and community dynamics across abiotic gradients. [ABSTRACT FROM AUTHOR]

The influential rare biosphere concept in microbial ecology focuses on taxonomic scarcity and treats functional rarity implicitly. Microbes can possess functions distinct from other taxa in a community and can be present at high or low abundances. We define functionally rare microbes as possessing distinct functions and being numerically scarce. Functionally rare microbes can contribute disproportionately to ecosystem multifunctionality. The functional rarity concept helps to mechanistically connect microbial functional diversity, ecosystem functioning, and evolutionary processes. It also highlights the need for conservation of rare functions in microbial communities. The influential concept of the rare biosphere in microbial ecology has underscored the importance of taxa occurring at low abundances yet potentially playing key roles in communities and ecosystems. Here, we refocus the concept of rare biosphere through a functional trait-based lens and provide a framework to characterize microbial functional rarity, a combination of numerical scarcity across space or time and trait distinctiveness. We demonstrate how this novel interpretation of the rare biosphere, rooted in microbial functions, can enhance our mechanistic understanding of microbial community structure. It also sheds light on functionally distinct microbes, directing conservation efforts towards taxa harboring rare yet ecologically crucial functions. [ABSTRACT FROM AUTHOR]

The list of standard abbreviations for JDS is available at adsa.org/jds-abbreviations-24. Nonstandard abbreviations are available in the Notes. In modern breeding systems, cows are subjected to many stress factors. Animals fed a high-grain diet may have a decreased rumen pH, which would lead to subacute ruminal acidosis syndrome. The aim of this study was to investigate the evolution of microbial community composition in cows undergoing a dietary stress challenge. Twelve cows were subjected to a challenge period that consisted of a rapid change of ration, from a normal (45.4:54.6 forage:concentrate) to a high-grain content diet (24.8:75.2 forage:concentrate) to induce subacute ruminal acidosis. Individual rumen fluid content samples were collected before (T0) and during the challenge (T3, T14, T28). The DNA from rumen contents was extracted, purified, and sequenced to evaluate bacterial populations, and sequencing was performed on Illumina MiSeq. The effect of animal conditions on rumen microbial community was quantified through a linear mixed model. The acidogenic diet created 2 main clusters: ruminal hypomotility (RH) and milk fat depression (MFD). The microbial composition did not differ in T0 between the 2 groups, whereas during the challenge Ruminococcus spp., Treponema spp., Methanobrevibacter spp., and Methanosphaera spp. concentrations increased in RH cows; and Succinivibrio spp. and Butyrivibrio spp. concentrations increased in MFD cows. Prevotella spp. and Ruminococcus spp. were negatively correlated, whereas the Christenellaceae family was positively correlated with both Methanobrevibacter spp. and Methanosphaera spp. Moreover, the same diet affected cows' microbiota composition differently, underlying the impact of the host effect. Other studies are necessary to deepen the relationship between microbiota composition and host. [ABSTRACT FROM AUTHOR]

The list of standard abbreviations for JDS is available at adsa.org/jds-abbreviations-24. Nonstandard abbreviations are available in the Notes. Traditional fermented milks are produced through an inoculation process that involves the deliberate introduction of microorganisms that have been adapted and perpetuated across successive generations. However, the changes in the microbiota of traditional fermented milk during long-term inoculation fermentation in a laboratory environment remain unclear. In this study, we collected 5 samples of traditional fermented milk samples from 5 different counties in Tibet (3 kurut products) and Xinjiang (2 tarag products) of China, which served as starter cultures for a 9-mo continuous inoculation fermentation experiment. We analyzed the inter- and intrapopulation variations in the microbial communities of the collected samples, representing their macrodiversity and microdiversity, using shotgun metagenomic sequencing. Across all samples, we obtained a total of 186 high-quality metagenomic-assembled genomes, including 7 genera and 13 species with a relative abundance of more than 1%. The majority of these genomes were annotated as Lactobacillus helveticus (60.46%), Enterococcus durans (9.52%), and Limosilactobacillus fermentum (6.23%). We observed significant differences in species composition and abundance among the 5 initial inoculants. During the long-term inoculation fermentation, we found an overall increasing trend in species diversity, composition, and abundances of carbohydrate metabolism module-encoding genes in the fermented milk bacterial metagenome, while the fermented milk virome exhibited a relatively narrow range of variation. Lactobacillus helveticus, a dominant species in traditional fermented milk, displayed high stability during the long-term inoculation fermentation. Our study provides valuable insights for the industrial production of traditional fermented milk. [ABSTRACT FROM AUTHOR]

Soil suppressiveness can reduce the damage by plant parasitic nematodes (PPN) in agricultural soils and is conveyed by the activity of soil microorganisms. While natural suppressiveness has been reported, it is still poorly understood if soil suppressiveness can be elicited by manipulating the soil microbial community. In the present study we assessed the number of the Pratylenchus penetrans (Pp) and the bacterial and fungal community composition over 7 years in a long-term soil health experiment. The field experiment consisted of an organic and conventional agricultural land management system and three soil health treatments (SHT): an untreated control (CT), anaerobic disinfestation (AD) and a combination of marigold cover cropping, compost and chitin amendment (CB). The land management systems were kept continuously, while the soil health treatments were applied only twice in seven years. The microbial community significantly differed between the organic and conventional system, but there was no significant difference in Pp numbers between the two systems. However, both the CB treatment and to a lesser extent the AD treatment reduced Pp numbers and increased yield with the effect being the strongest in the years immediately after the treatment. Accordingly, both the bacterial and fungal community differed significantly between the treatments, the differences being largest in the years after the treatments. Notably, the CB treatment elicited both long-term changes in the microbial community and a reduction of Pp numbers lasting for at least three years. These results indicated that a combination of treatments can lead to an altered soil microbial community in combination with persisting suppressiveness of Pp. [ABSTRACT FROM AUTHOR]

Legume/cereal intercropping is an example of classic nitrogen-efficient planting that can effectively improve crop yield and nutrient-utilization efficiency. However, the interaction between rhizosphere microorganisms and rhizodeposition and the related ecological mechanisms remain unclear. We conducted a pot experiment using 13CO2 continuous labeling, DNA stable isotope probe technology, high-throughput sequencing, and the carbon-nitrogen-phosphorus functional gene chip to effectively track rhizosphere-deposited C and compare the microorganisms that utilize this C pool in the rhizosphere of a soybean/maize intercropping system at 21 days after labeling. The relative abundance of Caldalkalibacillus and Nesterenkonia that use rhizosphere-deposited C was significantly higher in the soybean/maize intercropping system than in monocropped soybean, but there were no significant differences between intercropped and monocropped maize. The soybean/maize intercropping system altered the composition of the microbial community that utilizes rhizosphere-deposited C and reduced the community richness. Moreover, intercropping improved the expression of functional genes associated with carbon fixation (acsH and exg) and nitrous oxide reduction (nosZ1). Overall, by tracking the flow of C from plant photosynthetic products to root exudates, our research provides new insights into identifying the microbial communities that assimilate and deposit carbon in soil. [ABSTRACT FROM AUTHOR]

Background: Considered the second largest and most diverse microbiome after the gut, the human oral ecosystem is complex with diverse and niche‐specific microorganisms. Although evidence is growing for the importance of oral microbiome in supporting a healthy immune system and preventing local and systemic infections, the influence of craniomaxillofacial (CMF) trauma and routine reconstructive surgical treatments on community structure and function of oral resident microbes remains unknown. CMF injuries affect a large number of people, needing extensive rehabilitation with lasting morbidity and loss of human productivity. Treatment efficacy can be complicated by the overgrowth of opportunistic commensals or multidrug‐resistant pathogens in the oral ecosystem due to weakened host immune function and reduced colonization resistance in a dysbiotic oral microbiome. Aims: To understand the dynamics of microbiota's community structure during CMF injury and subsequent treatments, we induced supra‐alveolar mandibular defect in Hanford miniature swine (n = 3) and compared therapeutic approaches of immediate mandibullar reconstructive (IMR) versus delayed mandibullar reconstructive (DMR) surgeries. Methods: Using bacterial 16S ribosomal RNA gene marker sequencing, the composition and abundance of the bacterial community of the uninjured maxilla (control) and the injured left mandibula (lingual and buccal) treated by DMR were surveyed up to 70‐day post‐wounding. For the injured right mandibula receiving IMR treatment, the microbial composition and abundance were surveyed up to 14‐day post‐wounding. Moreover, we measured sera level of biochemical markers (e.g., osteocalcin) associated with bone regeneration and healing. Computed tomography was used to measure and compare mandibular bone characteristics such as trabecular thickness between sites receiving DMR and IMR therapeutic approaches until day 140, the end of study period. Results: Independent of IMR versus DMR therapy, we observed similar dysbiosis and shifts of the mucosal bacteria residents after CMF injury and/or following treatment. There was an enrichment of Fusobacterium, Porphyromonadaceae, and Bacteroidales accompanied by a decline in Pasteurellaceae, Moraxella, and Neisseria relative abundance in days allotted for healing. We also observed a decline in species richness and abundance driven by reduction in temporal instability and inter‐animal heterogeneity on days 0 and 56, with day 0 corresponding to injury in DMR group and day 56 corresponding to delayed treatment for DMR or injury and immediate treatment for the IMR group. Analysis of bone healing features showed comparable bone‐healing profiles for IMR vs. DMR therapeutic approach. [ABSTRACT FROM AUTHOR]

Humic acid (HA) is a typical refractory organic matter, so it is of great significance to investigate its effect on the performance of Anammox granular sludge. When the dosage of HA ≤ 50 mg/L, HA promotes the total nitrogen removal rate (NRR) to 1.45 kg/(m3·day). When HA was between 50 and 100 mg/L, the NRR of Anammox was stable. At this time, the adsorption of HA causes the sludge to gradually turn from red to brown, but the activities of heme and enzymes showed that its capacity was not affected. When HA levels reached 250 mg/L, the NRR dropped to 0.11 kg/(m3·day). Moderate HA levels promoted the release of extracellular polymeric substance (EPS), but excessive HA levels lead to a decrease in EPS concentrations. HA inhibited Anammox activity, which indirectly hindered the transmission of substrate and accumulated substrate toxicity. Although HA promoted the increase of heterotrophic microbial abundance in Anammox system, the microbial diversity decreased gradually. With the increase of HA concentration, the abundance of Candidatus_Brocadia , the main functional microorganism of Anammox system, decreased gradually, while the abundance of Candidatus_Kuenenia increased gradually. [ABSTRACT FROM AUTHOR]

• Novel carbon source and corncob had better denitrification efficiency than polycaprolactone and polyvinyl alcohol-sodium alginate. • The taxonomical composition of bacterial, fungal and archaeal communities can be altered by types of solid carbon source. • Some fungi and archaea species were conducive to solid-phase denitrification (SPD) systems. • Co-occurring network showed some potential collaboration between bacterial fungal and archaeal communities in SPD systems. • Amplicon sequence variant (ASV) can identify more taxonomies that operational taxonomic unit (OTU) cannot in this study. There is a lack of understanding about the bacterial, fungal and archaeal communities' composition of solid-phase denitrification (SPD) systems. We investigated four SPD systems with different carbon sources by analyzing microbial gene sequences based on operational taxonomic unit (OTU) and amplicon sequence variant (ASV). The results showed that the corncob-polyvinyl alcohol sodium alginate-polycaprolactone (CPSP, 0.86±0.04 mg NO 3 −-N/(g·day)) and corncob (0.85±0.06 mg NO 3 −-N/(g·day)) had better denitrification efficiency than polycaprolactone (PCL, 0.29±0.11 mg NO 3 −-N/(g·day)) and polyvinyl alcohol-sodium alginate (PVA-SA, 0.24±0.07 mg NO 3 −-N/(g·day)). The bacterial, fungal and archaeal microbial composition was significantly different among carbon source types such as Proteobacteria in PCL (OTU: 83.72%, ASV: 82.49%) and Rozellomycota in PVA-SA (OTU: 71.99%, ASV: 81.30%). ASV methods can read more microbial units than that of OTU and exhibit higher alpha diversity and classify some species that had not been identified by OTU such as Nanoarchaeota phylum, unclassified_ f_ Xanthobacteraceae genus, etc., indicating ASV may be more conducive to understand SPD microbial communities. The co-occurring network showed some correlation between the bacteria fungi and archaea species, indicating different species may collaborate in SPD systems. Similar KEGG function prediction results were obtained in two bioinformatic methods generally and some fungi and archaea functions should not be ignored in SPD systems. These results may be beneficial for understanding microbial communities in SPD systems. [Display omitted] [ABSTRACT FROM AUTHOR]

Deep-sea trenches representing an intriguing ecosystem for exploring the survival and evolutionary strategies of microbial communities in the highly specialized deep-sea environments. Here, 29 metagenomes were obtained from sediment samples collected from Kermadec and Diamantina trenches. Notably, those samples covered a varying sampling depths (from 5321 m to 9415 m) and distinct layers within the sediment itself (from 0~40 cm in Kermadec trench and 0~24 cm in Diamantina trench). Through metagenomic binning process, we reconstructed 982 metagenome assembled genomes (MAGs) with completeness >60% and contamination <5%. Within them, completeness of 351 MAGs were >90%, while an additional 331 were >80%. Phylogenomic analysis for the MAGs revealed nearly all of them were distantly related to known cultivated isolates. The abundant bacterial MAGs affiliated to phyla of Proteobacteria, Planctomycetota, Nitrospirota, Acidobacteriota, Actinobacteriota, and Chlorofexota, while the abundant archaeal phyla affiliated with Nanoarchaeota and Thermoproteota. These results provide a dataset available for further interrogation of diversity, distribution and ecological function of deep-sea microbes existed in the trenches. [ABSTRACT FROM AUTHOR]

Background: Bacteria, Archaea, and Microeukaryotes comprise taxonomic domains that interact in mediating biogeochemical cycles in coastal waters. Many studies have revealed contrasting biogeographic patterns of community structure and assembly mechanisms in microbial communities from different domains in coastal ecosystems; however, knowledge of specific biogeographic patterns on microbial co-occurrence relationships across complex coastal environmental gradients remains limited. Using a dense sampling scheme at the regional scale, SSU rRNA gene amplicon sequencing, and network analysis, we investigated intra- and inter-domain co-occurrence relationships and network topology-based biogeographic patterns from three microbial domains in coastal waters that show environmental gradients across the inshore-nearshore-offshore continuum in the East China Sea. Results: Overall, we found the highest complexity and connectivity in the bacterial network, the highest modularity in the archaeal network, and the lowest complexity, connectivity, and modularity in the microeukaryotic network. Although microbial co-occurrence networks from the three domains showed distinct topological features, they exhibited a consistent biogeographic pattern across the inshore-nearshore-offshore continuum. Specifically, the nearshore zones with intermediate levels of terrestrial impacts reflected by multiple environmental factors (including water temperature, salinity, pH, dissolved oxygen, and nutrient-related parameters) had a higher intensity of microbial co-occurrence for all three domains. In contrast, the intensity of microbial co-occurrence was weaker in both the inshore and the offshore zones at the two ends of the environmental gradients. Archaea occupied a central position in the microbial inter-domain co-occurrence network. In particular, members of the Thaumarchaeota Marine Group I (MGI, now placed within the Family Nitrosopumilaceae of the Phylum Thermoproteota) appeared to be the hubs in the biogeographic shift between inter-domain network modules across environmental gradients. Conclusions: Our work offers new insights into microbial biogeography by integrating network features into biogeographic patterns, towards a better understanding of the potential of microbial interactions in shaping biogeographic patterns of coastal marine microbiota. [ABSTRACT FROM AUTHOR]

Using oral swabs to collect the remnants of stomach content regurgitation during rumination in dairy cows can replicate up to 70% of the ruminal bacterial community, offering potential for broad-scale population-based studies on the rumen microbiome. The swabs collected from dairy cows often vary widely with respect to sample quality, likely due to several factors such as time of sample collection and cow rumination behavior, which may limit the ability of a given swab to accurately represent the ruminal microbiome. One such factor is the color of the swab, which can vary significantly across different cows. Here, we hypothesize that darker-colored swabs contain more rumen contents, thereby better representing the ruminal bacterial community than lightercolored swabs. To address this, we collected oral swabs from 402 dairy cows and rumen samples from 13 cannulated cows on a research farm in Wisconsin, United States and subjected them to 16S rRNA sequencing. In addition, given that little is known about the ability of oral swabs to recapitulate the ruminal fungal community, we also conducted ITS sequencing of these samples. To correlate swab color to the microbiota we developed and utilized a novel imaging approach to colorimetrically quantify each swab from a range of light to dark. We found that swabs with increasing darkness scores were significantly associated with increased bacterial alpha diversity (p < 0.05). Lighter swabs exhibited greater variation in their community structure, with many identified amplicon sequence variants (ASVs) categorized as belonging to known bovine oral and environmental taxa. Our analysis of the fungal microbiome found that swabs with increasing darkness scores were associated with decreased alpha diversity (p < 0.05) and were also significantly associated with the ruminal solids fungal community, but not with the ruminal liquid community. Our study refines the utility of oral swabs as a useful proxy for capturing the ruminal microbiome and demonstrates that swab color is an important factor to consider when using this approach for documenting both the bacterial and fungal communities. [ABSTRACT FROM AUTHOR]

The intricate relationship between cancer and bacteria has garnered increasing attention in recent years. While traditional cancer research has primarily focused on tumor cells and genetic mutations, emerging evidence highlights the significant role of microbial communities within the tumor microenvironment in cancer development and progression. This review aims to provide a comprehensive overview of the current understanding of the complex interplay between cancer and bacteria. We explore the diverse ways in which bacteria influence tumorigenesis and tumor behavior, discussing direct interactions between bacteria and tumor cells, their impact on tumor immunity, and the potential modulation of the tumor microenvironment. Additionally, we delve into the mechanisms through which bacterial metabolites and extracellular products May affect cancer pathways. By conducting a thorough analysis of the existing literature, we underscore the multifaceted and intricate relationship between bacteria and cancer. Understanding this complex interplay could pave the way for novel therapeutic approaches and preventive strategies in cancer treatment. [ABSTRACT FROM AUTHOR]

Introduction: Carotenoids are important precursors of various aroma components in tobacco and play an important role in the sensory quality of tobacco. Phaffia rhodozyma is a species of Xanthophyllomyces capable of synthesizing a highly valuable carotenoid-astaxanthin, but has not yet been used in improving tobacco quality. Methods: The dynamic changes of microbial community and metabolites during tobacco fermentation were analyzed in combination with microbiome and metabolome, and the quality of tobacco after fermentation was evaluated by sensory scores. Results: P. rhodozyma could grow and produce carotenoids in tobacco extract, with a maximum biomass of 6.50 g/L and a maximum carotenoid production of 36.13 mg/L at 100 g/L tobacco extract. Meanwhile, the correlation analysis combined with microbiome and metabolomics showed that P. rhodozyma was significantly positively correlated with 11 metabolites such as 6-hydroxyluteolin and quercetin. Furthermore, the contents of alcohols, ketones and esters, which were important aromatic components in fermented tobacco, reached 77.57 μg/g, 58.28 μg/g and 73.51 μg/g, increasing 37.39%, 265.39% and 266.27% compared to the control group, respectively. Therefore, the aroma and flavor, and taste scores of fermented tobacco increased by 0.5 and 1.0 points respectively. Discussion: This study confirmed that P. rhodozyma fermentation could effectively improve the sensory evaluation of tobacco, and provided a novel microbial fermentation method to improve tobacco quality. [ABSTRACT FROM AUTHOR]

Corn (C), wheat (W), and paddy rice (PR) are important energy sources and are commonly used in feed production for swine. This study mainly focuses on the variation and regularities of microbiota and metabolites in the gastrointestinal tract (GIT) of pigs in response to C, W, and PR. A total of 18 pigs were allotted into three dietary groups with six replicated pigs and received diets containing C, W, or PR as the sole energy source, respectively. The results showed that digestive parts significantly affected the diversity of microbial communities. Cereal grain sources significantly influenced the β-diversity of microbial communities in the colon and rectum. Campylobacterota and Proteobacteria are mainly distributed in the duodenum, Lactobacillus in the jejunum, and Bacteroidota in the colon and rectum. The W diet increased the Bacteroidota, Spirochaetota, and Prevotellaceae_NK3B31_group abundances and showed the highest concentrations of all short-chain fatty acids (SCFAs) in the hindgut. Fibrobacterota, Bacteroidota, Spirochaetota, Prevotellaceae_NK3B31_group, Prevotella, and Treponema in the colon or rectum were positively correlated with acetate, propionate, butyrate, and total SCFAs. These findings suggested that aerobic bacteria and facultative anaerobes in the foregut will gradually be replaced by anaerobes in the hindgut. The W diet had the best fermentability and was beneficial to the colonization of microbial communities that mainly used carbohydrates. The hindgut flora of the PR diet group may be more balanced with fewer potential pathogenic bacteria. Many microbial communities have been identified to contribute positively to the SCFA production of the hindgut. Collectively, our study revealed the spatial variation regularities of GIT microbial communities in an adult pig model and provided new insights into GIT microbiota and responses of metabolites to cereal grain diets. [ABSTRACT FROM AUTHOR]

Background: The relationship between dysbiosis of the gastrointestinal microbiota and gastric cancer (GC) has been extensively studied. However, microbiota alterations in GC patients vary widely across studies, and reproducible diagnostic biomarkers for early GC are still lacking in multiple populations. Thus, this study aimed to characterize the gastrointestinal microbial communities involved in gastric carcinogenesis through a metaanalysis of multiple published and open datasets. Methods: We analyzed 16S rRNA sequencing data from 1,642 gastric biopsy samples and 394 stool samples across 11 independent studies. VSEARCH, QIIME and R packages such as vegan, phyloseq, cooccur, and random forest were used for data processing and analysis. PICRUSt software was employed to predict functions. Results: The α-diversity results indicated significant differences in the intratumoral microbiota of cancer patients compared to non-cancer patients, while no significant differences were observed in the fecal microbiota. Network analysis showed that the positive correlation with GC-enriched bacteria increased, and the positive correlation with GC-depleted bacteria decreased compared to healthy individuals. Functional analyses indicated that pathways related to carbohydrate metabolism were significantly enriched in GC, while biosynthesis of unsaturated fatty acids was diminished. Additionally, we investigated non-Helicobacter pylori (HP) commensals, which are crucial in both HP-negative and HP-positive GC. Random forest models, constructed using specific taxa associated with GC identified from the LEfSe analysis, revealed that the combination of Lactobacillus and Streptococcus included alone could effectively discriminate between GC patients and healthy individuals in fecal samples (area under the curve (AUC) = 0.7949). This finding was also validated in an independent cohort (AUC = 0.7712). Conclusions: This study examined the intratumoral and fecal microbiota of GC patients from a dual microecological perspective and identified Lactobacillus, Streptococcus, Roseburia, Faecalibacterium and Phascolarctobacterium as intratumoral and intestinal-specific co-differential bacteria. Furthermore, it confirmed the validity of the combination of Lactobacillus and Streptococcus as GC-specific microbial markers across multiple populations, which may aid in the early non-invasive diagnosis of GC. [ABSTRACT FROM AUTHOR]

Landfill leachate, a complex mixture resulting from decomposing waste, contains suspended and dissolved organic and inorganic compounds. This nutrient-rich environment facilitates the growth of diverse microbial communities that can utilize these compounds for sustenance. Rhodotorula mucilaginosa is a yeast with great potential in the field of biotechnology due to its ability to utilize diverse substrates and its strong resistance to environmental stress. This study was aimed at investigating the potential of R. mucilaginosa, a yeast strain isolated from landfill environments, for biofuel production and simultaneous pollutant reduction in leachate. Batch cultivations were conducted using leachate as the sole growth medium. Cultivation was conducted for 2, 4, 6, and 8 days to analyse the lipids from R. mucilaginosa biomass and the degradation of pollutants in the resulting leachate. Additionally, the fuel properties were determined to assess the quality of the biodiesel produced from R. mucilaginosa lipids. The obtained quality was compared with the American Society for Testing and Materials (ASTM D6751), the Indonesian National Standard (SNI 8968:2021), and the fatty acid methyl ester (FAME) derived from palm oil. Results demonstrated significant lipid accumulation by R. mucilaginosa, reaching 19% (w/w) after 144 hours (6 days) of cultivation. Gas chromatography-mass spectrometry (GC-MS) analysis revealed a FAME profile dominated by C16 and C18 fatty acids, suitable for biodiesel production. Concurrently, substantial reductions in leachate pollutant levels were observed, with decreases of 40.43% for chemical oxygen demand (COD), 86% for phosphate, 90% for ammonia, 53% for nitrate, and 64% for nitrite. These findings highlight the potential of R. mucilaginosa, isolated from landfill leachate, as a promising bioremediation agent for wastewater treatment and a sustainable source of lipids for renewable energy production. [ABSTRACT FROM AUTHOR]

The pernicious nature of low-quality sequencing data warrants improvement in the bioinformatics workflow for profiling microbial diversity. The conventional merging approach, which drops a copious amount of sequencing reads when processing low-quality amplicon data, requires alternative methods. In this study, a computational workflow, a combination of merging and direct-joining where the paired-end reads lacking overlaps are concatenated and pooled with the merged sequences, is proposed to handle the low-quality amplicon data. The proposed computational strategy was compared with two workflows; the merging approach where the paired-end reads are merged, and the direct-joining approach where the reads are concatenated. The results showed that the merging approach generates a significantly low number of amplicon sequences, limits the microbiome inference, and obscures some microbial associations. In comparison to other workflows, the combination of merging and direct-joining strategy reduces the loss of amplicon data, improves the taxonomy classification, and importantly, abates the misleading results associated with the merging approach when analysing the low-quality amplicon data. The mock community analysis also supports the findings. In summary, the researchers are suggested to follow the merging and direct-joining workflow to avoid problems associated with low-quality data while profiling the microbial community structure. [ABSTRACT FROM AUTHOR]

Effective removal of ammonia, nitrate, and intermediate nitrite is a challenge faced by highly dissolved oxygen (DO) recirculating aquaculture systems (RAS). This study investigated the effect of DO concentrations (Group A, DO 3.15 ± 0.12 mg/L, Group B, DO 4.43 ± 0.15 mg/L, Group C, DO 6.52 ± 0.35 mg/L, Group D, and DO 7.86 ± 0.55 mg/L) on the simultaneous nitrification and denitrification (SND) of aquaculture seawater using poly (3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) as a biofilm carrier and solid-phase denitrification (SPD) carbon source. Ammonia and nitrate were simultaneously removed in all the PHBV-supported SPD systems. Ammonia in Group C had the highest removal rate (5.72 mg/(L·h)), whereas nitrate and nitrite in Group A were completely removed at 4 and 5 h, respectively. The continuous release of PHBV provided carbon sources for denitrification. High throughout sequencing showed that Proteobacteria, Bacteroidetes, Desulfobacterota, and Chloroflexi at the phylum level, and Marinobacter, Shewanella, and Pseudomonas at the genus level exhibited unique relative abundances under varying DO concentrations. The nitrification genes in Group C showed the highest expression. Denitrification genes in Group A were enriched. The relative expression of nitrogen-transforming genes further demonstrated the results for water quality and the microbial community. DO concentration affected the efficiency of the nitrogen transformation pathway in the PHBV-supported SPD system. [ABSTRACT FROM AUTHOR]

Background Aims Methods Results Conclusions Sewage sludge biochar has been widely used in agriculture for various purposes; however, knowledge about its residual effect on the soil microbial community is limited.This study aimed to evaluate changes in the microbial community 5 years after the application of sewage sludge biochar.Biochar was produced from sewage sludge obtained at a wastewater treatment pyrolyzed at 300°C (Biochar300) and 500°C (Biochar500). Both biochar treatments were applied in corn fields for two growing seasons (2014/2015; 2015/2016). Biochar was not applied from the third (2016/2017) to the seventh (2020/2021) growing season to assess the residual effect. Soil samples were collected after harvesting in 2020/2021 growing season, therefore in the fifth year subject to the residual effects of biochar. The microbial community was evaluated by accessing bacterial and fungal groups using DNA techniques. Amplicon sequencing analysis was performed with the samples by Illumina MiSeq 250 bp.At genus level, the Lachnospira, Faecalibacterium, Bacteroides, Epulopiscium, and Parabacteroides were affected by Biochar500. Furthermore, at upper levels of taxonomy, this biochar treatment increased the relative abundance of bacterial classes Clostridiaceae and Bacteroidia and the fungal families Chaetomiaceae and Aspergillaceae. Concerning the relationship between microbial community and soil chemical properties, soil phosphorus (P) and calcium (Ca) were significantly affected by biochar treatments within the bacterial community; the fungal ones affected significantly soil P and potential acidity (H + Al).Even under the residual effect of 5 years, the application of biochar altered the microbial community on corn plantation, especially concerning on the richness and the abundance of some groups. Biochar500 was the most responsive among the treatments. [ABSTRACT FROM AUTHOR]

Background: The Calakmul Biosphere Reserve (CBR) is known for its rich animal and plant biodiversity, yet its microbial communities remain largely unknown. The reserve does not possess permanent bodies of water; nevertheless, seasonal depressions associated with fractures create wetlands, known locally as aguadas. Given the recent construction of the Maya train that crosses the CRB, it is essential to assess the biodiversity of its microorganisms and recognize their potential as a valuable source of goods. This evaluation is pivotal in mitigating potential mismanagement of the forest ecosystem. To enhance comprehension of microbial communities, we characterized the microbiota in three different wetlands. Ag-UD1 and Ag-UD2 wetlands are located in a zone without human disturbances, while the third, Ag-SU3, is in a semi-urbanized zone. Sampling was carried out over three years (2017, 2018, and 2019), enabling the monitoring of spatiotemporal variations in bacterial community diversity. The characterization of microbiome composition was conducted using 16S rRNA metabarcoding. Concurrently, the genomic potential of select samples was examined through shotgun metagenomics. Results: Statistical analysis of alpha and beta diversity indices showed significant differences among the bacterial communities found in undisturbed sites Ag-UD1 and Ag-UD2 compared to Ag-SU3. However, no significant differences were observed among sites belonging to the undisturbed area. Furthermore, a comparative analysis at the zone level reveals substantial divergence among the communities, indicating that the geographic location of the samples significantly influences these patterns. The bacterial communities in the CBR wetlands predominantly consist of genera from phyla Actinobacteria, Acidobacteria, and Proteobacteria. Conclusion: This characterization has identified the composition of microbial communities and provided the initial overview of the metabolic capacities of the microbiomes inhabiting the aguadas across diverse conservation zones. The three sites exhibit distinct microbial compositions, suggesting that variables such as chemical composition, natural and anthropogenic disturbances, vegetation, and fauna may play a pivotal role in determining the microbial structure of the aguadas. This study establishes a foundational baseline for evaluating the impact of climatic factors and human interventions on critical environments such as wetlands. [ABSTRACT FROM AUTHOR]

Recent advancements in next-generation sequencing have revolutionized our understanding of the human microbiome. Despite this progress, challenges persist in comprehending the microbiome's influence on disease, hindered by technical complexities in species classification, abundance estimation, and data compositionality. At the same time, the existence of macroecological laws describing the variation and diversity in microbial communities irrespective of their environment has been recently proposed using 16s data and explained by a simple phenomenological model of population dynamics. We here investigate the relationship between dysbiosis, i.e. in unhealthy individuals there are deviations from the "regular" composition of the gut microbial community, and the existence of macro-ecological emergent law in microbial communities. We first quantitatively reconstruct these patterns at the species level using shotgun data, and addressing the consequences of sampling effects and statistical errors on ecological patterns. We then ask if such patterns can discriminate between healthy and unhealthy cohorts. Concomitantly, we evaluate the efficacy of different statistical generative models, which incorporate sampling and population dynamics, to describe such patterns and distinguish which are expected by chance, versus those that are potentially informative about disease states or other biological drivers. A critical aspect of our analysis is understanding the relationship between model parameters, which have clear ecological interpretations, and the state of the gut microbiome, thereby enabling the generation of synthetic compositional data that distinctively represent healthy and unhealthy individuals. Our approach, grounded in theoretical ecology and statistical physics, allows for a robust comparison of these models with empirical data, enhancing our understanding of the strengths and limitations of simple microbial models of population dynamics. Author summary: In this study, we explore emerging ecological properties in gut microbiomes. Our aim here is to determine whether these patterns can be informative of the gut microbiome (healthy or diseased) and unveil essential ingredients driving its population dynamics. Leveraging on metagenomic data and interpretable statistical models based on ecological processes, we show that not all ecological patterns are informative to characterize its states, while few are (e.g., species diversity). Eventually, thanks to the ecological interpretability of the inferred models' parameters, our analysis provides insights into the role of environmental fluctuations and carrying capacities of the gut microbiomes in both health and disease. This study offers valuable knowledge, bridging theoretical concepts with practical implications for human health. [ABSTRACT FROM AUTHOR]

Phyllosphere microorganisms execute important ecological functions including supporting host plant growth, enhancing host resistance to abiotic stresses, and promoting plant diversity. How leaf developmental stages affect plant-microbiome interactions and phyllosphere microbial community assembly and diversity is poorly understood. In this study, we utilized amplicon sequencing of 16S rRNA and ITS genes to investigate the composition and diversity of microbial communities across different leaf developmental stages of rubber trees. Our findings reveal that endophytic microbial communities, particularly bacterial communities, are more influenced by leaf senescence than by epiphytic communities. The high abundance of metabolism genes in the endosphere of yellow leaves contributes to the degradation and nutrient relocation processes. Nutrient loss leads to a higher abundance of α-Proteobacteria (r-selected microorganisms) in the yellow leaf endosphere, thereby promoting stochastic community assembly. As leaves age, the proportion of microorganisms entering the inner layer of leaves increases, consequently enhancing the diversity of microorganisms in the inner layer of leaves. These results offer insights into the mechanisms governing community assembly and diversity of leaf bacteria and fungi, thereby advancing our understanding of the evolving functions of microbial communities during leaf senescence in general, and for an important tropical crop species in particular. Leaf senescence has significant impacts on the composition, diversity, assembly, and functions of phyllosphere microbiomes, especially impacting endophytic bacterial communities. [ABSTRACT FROM AUTHOR]

Microbiota associated with host–parasite relationships offer an opportunity to explore interactions among plants, parasites, and microbes, thereby contributing to the overall complexity of community structures. The dynamics of ecological interactions between parasitic plants and their hosts in arid environments remain largely understudied, especially in Africa. This study aimed to examine the bacterial communities of Cuscuta epithymum L. (clover dodder), an epiphytic parasitic plant, and its host, Ziziphus lotus L. (jujuba), in an arid environment. Our goal was to uncover the ecological complexities of microbial communities within the framework of plant–plant interactions. We conducted a comprehensive analysis of the bacterial composition and diversity within populations of the C. epithymum parasite, the infected- and non-infected jujuba host, and their interface at the shoots of the host. This involved amplicon sequencing, targeting the V5–V6 regions of the 16S rRNA gene. A total of 5680 amplicon sequence variants (ASVs) were identified, with Pseudomonadota, Bacillota, and Actinobacteriota being prevalent phyla. Among the bacterial communities, three genera were dominant: Cutibacterium, Staphylococcus, and Acinetobacter. Interestingly, analyses of alpha-diversity (p = 0.3 for Shannon index and p = 0.5 for Simplon index) and beta-diversity (PERMANOVA, with p-values of 0.6 and 0.3) revealed no significant differences between Cuscuta-infected and non-infected jujube shrubs, suggesting a shared shoot endophytic bacteriome. This finding advances our comprehension of microbial communities linked to plant–parasite interactions in the arid environments of Africa. Further research on various hosts is required to confirm plant-to-plant bacterial transmission through Cuscuta infection. Additionally, studies on functional diversity, cytology, ecophysiology and the mechanisms by which bacterial communities transferred between host and parasite are necessary. [ABSTRACT FROM AUTHOR]

Summary Interactions between plants and microorganisms are pivotal for plant growth and productivity. Several plant molecular mechanisms that shape these microbial communities have been identified. However, the importance of nitric oxide (NO) produced by plants for the associated microbiota remains elusive. Using Arabidopsis thaliana isogenic mutants overproducing NO (nox1, NO overexpression) or down‐producing NO (i.e. nia1nia2 impaired in the expression of both nitrate reductases NR1/NIA1 and NR2/NIA2; the 35s::GSNOR1 line overexpressing nitrosoglutathione reductase (GSNOR) and 35s::AHB1 line overexpressing haemoglobin 1 (AHB1)), we investigated how altered NO homeostasis affects microbial communities in the rhizosphere and in the roots, soil microbial activity and soil metabolites. We show that the rhizosphere microbiome was affected by the mutant genotypes, with the nox1 and nia1nia2 mutants causing opposite shifts in bacterial and fungal communities compared with the wild‐type (WT) Col‐0 in the rhizosphere and roots, respectively. These mutants also exhibited distinctive soil metabolite profiles than those from the other genotypes while soil microbial activity did not differ between the mutants and the WT Col‐0. Our findings support our hypothesis that changes in NO production by plants can influence the plant microbiome composition with differential effects between fungal and bacterial communities. [ABSTRACT FROM AUTHOR]

This study uses dual‐labeled (13C and 15N) stable isotope applications to examine microbial uptake and short‐term processing of carbon (C) and nitrogen (N) from organic and inorganic compounds in subtropical intertidal sediment. Four treatment applications were applied: (1) algal dissolved organic matter (DOM), (2) amino acid mixture, (3) glucose and NH4+$$ {\mathrm{NH}}_4^{+} $$, and (4) NaHCO3 and NH4+$$ {\mathrm{NH}}_4^{+} $$ to assess bioavailability effects on processing (1 vs. 2) and short‐term processing for OM fixed via microphytobenthos only (pennate diatom dominated) (4) vs. material taken up by the entire microbial community (3) across 24 h. 13C from algal‐DOM was preferentially used by the microbial community vs. 15N. At 24 h more 13C from algal‐DOM remained in microbial biomass indicating use of labeled precursor molecules to form biomass. Conversely, 13C from the amino acid treatment was not incorporated into biomass and was either rapidly respired to DIC or discarded as the in situ microbial community preferentially used and retained 15N from amino acids. Short‐term export of 13C as CO2 from glucose was lower than from microphytobenthos‐C, while retention of 15N from NH4+$$ {\mathrm{NH}}_4^{+} $$ was similar between treatments (3 and 4) despite doubling the application N concentration, suggesting potentially higher glucose‐stimulated 15N export via nitrification–denitrification that was not confirmed via flux measurements in this study. Despite careful site selection for similar tidal exposure and sediment types among the three estuaries, the uptake and processing of labeled substrate varied substantially between replicates and sites which challenged traditional statistical analysis. Disproportionate processing of substrates occurring in sediment hotspots of microbial activity can cause variability spanning orders of magnitude which was found to be widespread through comparison of our results against 19 previous studies in intertidal settings. Development of robust analytical techniques to handle variability from abiotic and biotic factors will allow greater clarity surrounding in situ biogeochemical processing in intertidal environments. [ABSTRACT FROM AUTHOR]

Background: Paddy soil is a typical soil type affected by anthropogenic management and factors related to natural soil formation. The evolution from mudflats to typical paddy soils can significantly affect the soil microecology. Previous studies have reported the evolution of soil physicochemical properties, microbes, and related soil environmental factors in a millennium paddy soil chronosequence. However, the potential biological mechanisms of changes in metabolites and microbes–metabolites interaction are poorly understood. Therefore, a combination of high-throughput sequencing and environmental pseudotargeted metabolomics techniques was adopted to explore the effects of the millennium paddy soil chronosequence on microbial communities, metabolites, and their functions and interactions. Results: The soil ecology changed greatly in the first 60 years of the transition from mudflat to paddy planting. Among the microbial communities, the response of the bacteria to the chronosequence was more sensitive than that of fungi. Among them, the bacterial communities of Proteobacteria, Bacteroidetes, Acidobacteria, and Nitrospirae exhibited regular succession over the chronosequence, but the fungal communities did not show regular changes. Bacterial function prediction revealed that the beginning of the critical stage of the evolution from mudflat to paddy soil involved the organic matter cycle and energy flow. In contrast, fungi were characterized mainly by pathogenic and saprophytic functions. The results of the principal component analysis of the metabolites revealed a similar pattern of change as that of the microbes. Seventy-five characteristic metabolites exhibited three trends of change during the development of the paddy soil chronosequence. Twenty-five differentially active metabolic pathways, including glyoxylate and dicarboxylate metabolism, starch and sucrose metabolism, and galactose metabolism, were enriched. In addition, correlation analysis revealed that long-chain fatty acids, short-chain fatty acids, phenolic acids, carbohydrates, and polyalcohols significantly regulate the microbial communities in paddy soil. Conclusions: Combining metabolome and microbiome has expanded the overall understanding of the development of paddy soil under anthropogenic management. During the development of a paddy soil chronosequence, the synergistic regulation of soil physicochemical properties and metabolites in the microbial community results in increased productivity. This study provides a new perspective on microbes and metabolites interaction. [ABSTRACT FROM AUTHOR]

Rhizosphere microbiotas play vital roles in resisting environmental stress, transforming soil nutrients, and promoting plant health, growth, and productivity. The effects of rhizosphere microbial community shaping and the characteristics and functions of keystone taxa on blueberries were comprehensively studied by examining the rhizobacteria of healthy old trees (O), young seedlings (OG), and poorly growing seedlings (OB) of O'Neal blueberries. Our results showed that rhizobacterial diversity followed the order OB > > OG > O, and the microbial community of OG was similar to that of O, while that of OB was distinctly different. The predominant rhizobacteria identified included Actinobacteria, Proteobacteria, Firmicutes, Chloroflexi, and Acidobacteria. Firmicutes were highly enriched in healthy blueberries, with Bacillus identified as a key genus that significantly enhanced blueberry growth when inoculated. Bradyrhizobium and Gaiellales were common core bacteria in the blueberry rhizosphere. In contrast, Acidobacteria were the predominant phylum in poorly growing OB, with the specific Vicinamibacterales-related and Latescibacterota-related genera acting as keystone taxa that shaped the microbial community. In addition, bacterial species in Vicinamibacterales might act as a potential pathogen predicted by BugBase. Taken together, these findings provide fundamental insights into the development of the blueberry rhizosphere microbial community and highlight the role of beneficial rhizobacteria, such as Bacillus, in enhancing blueberry growth. This knowledge could contribute to the exploitation of beneficial rhizobacteria and the prevention of pathogens in modern agriculture. [ABSTRACT FROM AUTHOR]

Over the last few decades, advancements in process safety and quality methods have been significantly improved, yet new challenges continue to emerge in the sustainable food supply chain. This study aimed to investigate some physicochemical and microbiological parameters impacting meat products, particularly cooked sausages, within a sustainable supply chain, focusing on quality, spoilage populations, and syneresis formation under vacuum conditions. A comprehensive analysis was conducted on 355 samples collected over four seasons using high-throughput sequencing (16S/ITS) and microbiological and physicochemical [pH and water activity (aw)] assessments. The microbial growth predictor MicroLab&lowbar;ShelfLife was employed, and multiple factor analysis (MFA) and agglomerative hierarchical clustering (AHC) were utilized to understand how these variables influence themicrobiome resilience of these products. Lactic and acetic acids were correlated with the microbiome of the sausages and the liquid coating covering them using metagenomic analyses. The study highlighted that 52% of the evaluated meat industries in southeastern Brazil are implementing including Trichosporon sp. and Candida sp., were identified as key genera influencing spoilage dynamics. In addition, Bacillus species emerged as dominant spoilage microorganisms, highlighting the need for new critical controls. This study demonstrates the impact of metagenomic approaches, including ITS and 16S amplicon sequencing, in revealing microbial community dynamics, storage temperature, and aw, which are essential for developing targeted interventions to enhance food safety and quality sustainably. [ABSTRACT FROM AUTHOR]

Multispecies microbial communities drive most ecosystems on Earth. Chemical and biological interactions within these communities can affect the survival of individual members and the entire community. However, the prohibitively high number of possible interactions within a microbial community has made the characterization of factors that influence community development challenging. Here, we report a Microbial Community Interaction (μCI) device to advance the systematic study of chemical and biological interactions within a microbial community. The μCI creates a combinatorial landscape made up of an array of triangular wells interconnected with circular wells, which each contains either a different chemical or microbial strain, generating chemical gradients and revealing biological interactions. Bacillus cereus UW85 containing green fluorescent protein provided the "target" readout in the triangular wells, and antibiotics or microorganisms in adjacent circular wells are designated the "variables." The μCI device revealed that gentamicin and vancomycin are antagonistic to each other in inhibiting the target B. cereus UW85, displaying weaker inhibitory activity when used in combination than alone. We identified three-member communities constructed with isolates from the plant rhizosphere that increased or decreased the growth of B. cereus. The μCI device enables both strain-level and community-level insight. The scalable geometric design of the μCI device enables experiments with high combinatorial efficiency, thereby providing a simple, scalable platform for systematic interrogation of three-factor interactions that influence microorganisms in solitary or community life. [ABSTRACT FROM AUTHOR]

Extracellular proteins play a significant role in shaping microbial communities which, in turn, can impact ecosystem function, human health, and biotechnological processes. Yet, for many ubiquitous microbes, there is limited knowledge regarding the identity and function of secreted proteins. Here, we introduce EXCRETE (enhanced exoproteome characterization by mass spectrometry), a workflow that enables comprehensive description of microbial exoproteomes from minimal starting material. Using cyanobacteria as a case study, we benchmark EXCRETE and show a significant increase over current methods in the identification of extracellular proteins. Subsequently, we show that EXCRETE can be miniaturized and adapted to a 96-well high-throughput format. Application of EXCRETE to cyanobacteria from different habitats (Synechocystis sp. PCC 6803, Synechococcus sp. PCC 11901, and Nostoc punctiforme PCC 73102), and in different cultivation conditions, identified up to 85% of all potentially secreted proteins. Finally, functional analysis reveals that cell envelope maintenance and nutrient acquisition are central functions of the predicted cyanobacterial secretome. Collectively, these findings challenge the general belief that cyanobacteria lack secretory proteins and suggest that multiple functions of the secretome are conserved across freshwater, marine, and terrestrial species. This study introduces EXCRETE (enhanced exoproteome characterization by mass spectrometry), a workflow that enables comprehensive description of microbial exoproteomes from minimal starting material. [ABSTRACT FROM AUTHOR]

Accurate characterization of the movement of water through catchments, particularly during precipitation event response, is critical for hydrological efforts such as contaminant transport modeling or prediction of extreme flows. Abiotic hydrogeochemical tracers are commonly used to track sources and ages of surface waters but provide limited details about transit pathways or the spatial dynamics of water storage and release. Alternatively, biotic material in streams is derived from thousands of taxa originating from a variety of environments within watersheds, including groundwater, sediment, and upslope terrestrial environments, and this material can be characterized with genetic sequencing and bioinformatics. We analyzed the stable water isotopes (δ18O and δ2H) and microbiome composition (16S rRNA gene amplicon sequencing) of the Marys River of western Oregon, USA during an early season storm to describe the processes, storage, and flowpaths that shape surface water hydrology. Stable water isotopes (δ18O and δ2H) typified an event response in which stream water is composed largely of 'old' water introduced to the catchment before the storm, a common though not well understood phenomenon. In contrast, microbial biodiversity spiked during the storm, consisting of early- and late-event communities clearly distinguishable from pre-event communities. We applied concentration-discharge (cQ) analysis to individual microbial taxa and found that most Alphaproteobacteria sequences were positively correlated (i.e., were mobilized) with discharge, whereas most sequences from phyla Gammaproteobacteria and Bacteroidota were negatively correlated with discharge (i.e., were diluted). Source predictions using the prokaryote habitat preference database ProkAtlas found that freshwater-associated microbes composed a smaller fraction of the microbial community during the stream rise and a larger fraction during the recession, while soil and biofilm-associated microbes increased during the storm and remained high during recession. This suggests that the "old" water discharged during the storm was likely stored and released from, or passed through, soil- and biofilm-rich environments, demonstrating that this approach adds new, biologically derived tracer information about the hydrologic pathways active during and after this event. Overall, this study demonstrates an approach for integrating information-rich DNA into water resource investigations, incorporating tools from both hydrology and microbiology to demonstrate that microbial DNA is useful not only as an indicator of biodiversity but also functions as an innovative hydrologic tracer. [ABSTRACT FROM AUTHOR]

Ectotherms have peculiar relationships with microorganisms. For instance, bacteria are recovered from the blood and internal organs of healthy teleosts. However, the presence of microbial communities in the healthy teleost brain has not been proposed. Here, we report a living bacterial community in the brain of healthy salmonids with bacterial loads comparable to those of the spleen and 1000-fold lower than in the gut. Brain bacterial communities share >50% of their diversity with gut and blood bacterial communities. Using culturomics, we obtained 54 bacterial isolates from the brains of healthy trout. Comparative genomics suggests that brain bacteria may have adaptations for niche colonization and polyamine biosynthesis. In a natural system, Chinook salmon brain microbiomes shift from juveniles to reproductively mature adults. Our study redefines the physiological relationships between the brain and bacteria in teleosts. This symbiosis may endow salmonids with a direct mechanism to sense and respond to environmental microbes. [ABSTRACT FROM AUTHOR]

AbstractIn this study, the impact of cobalt iron oxide(CoFe2O4) on the anaerobic digestion (AD) of food waste (FW) was investigated including the variations in pH, VFAs, ORP, Fe2+/Fe3+ concentrations, SCOD, dehydrogenase activity, methane production and microbial community structure. The results showed that CoFe2O4 had a positive effect on the anaerobic digestion of food waste. CoFe2O4 could promote the release of SCOD, increase the dehydrogenase concentration and reduce ORP resulting in an increase of methane production. At a CoFe2O4 concentration of 200 mg/L, the cumulative methane production reached to 414.75 mL/(gVS) which was increased by 79.1% compared to the control group(231.59 mL/(gVS)). Meanwhile, the variation of microbial community showed that CoFe2O4 could increase the relative abundance of Methanobacterium and the methane production pathway in the AD was shifted from acetoclastic to hydrogenotrophic. [ABSTRACT FROM AUTHOR]

Plant resource allocation strategies are thought to be largely a consequence of changing abiotic conditions and evolutionary history. However, biotic interactions also influence how a plant allocates resources. As a result, plants mediate indirect interactions between organisms above‐ and belowground through resource allocation. Neighboring plants can influence plant fitness directly through competition for resources, and indirectly by altering associated community interactions (associational effects), such as pollination, herbivory, and a suite of belowground interactions. Given the importance of community interactions for plant success, and the known ability for plant neighbors to change these interactions, the goal of this “pandemic project” was to understand how heterospecific plant neighbors alter plant resource allocation, whether this occurred through above‐ or belowground mechanisms, and whether this in turn alters biotic interactions and the relationship between a focal plant and its herbivore and soil community interactions. To do so, we established a common garden experiment, manipulating plant neighbor identity and the extent of interaction among neighbors (aboveground only, vs. above‐ and belowground interactions, using customized pot types), and measured changes to a focal plant and its biotic interactions over two growing seasons. We found evidence of both neighbor effects and pot type, showing that neighbor interactions affect a focal plant through both above‐ and belowground processes, and how the focal plant is affected depends on neighbor identity. Though neighbors did not directly alter herbivory or most soil microbial interactions, they did alter the relationship between belowground microbial communities and a plant response trait (specific leaf area). Plant resource allocation responses were reduced with time, showing the importance of extending experiments beyond a single growing season, and are an important consideration when making predictions about plant responses to changing conditions. This study contributes to a growing body of work showing how community contexts affect the above‐ and belowground interactions of a plant through plant resource allocation strategies. [ABSTRACT FROM AUTHOR]