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Background: Lake Bonney, which is divided into a west lobe (WLB) and an east lobe (ELB), is a perennially ice-covered lake located in the McMurdo Dry Valleys of Antarctica. Despite previous reports on the microbial community dynamics of ice-covered lakes in this region, there is a paucity of information on the relationship between microbial genomic diversity and associated nutrient cycling. Here, we applied gene- and genome-centric approaches to investigate the microbial ecology and reconstruct microbial metabolic potential along the depth gradient in Lake Bonney. Results: Lake Bonney is strongly chemically stratified with three distinct redox zones, yielding different microbial niches. Our genome enabled approach revealed that in the sunlit and relatively freshwater epilimnion, oxygenic photosynthetic production by the cyanobacterium Pseudanabaena and a diversity of protists and microalgae may provide new organic carbon to the environment. CO-oxidizing bacteria, such as Acidimicrobiales, Nanopelagicales, and Burkholderiaceae were also prominent in the epilimnion and their ability to oxidize carbon monoxide to carbon dioxide may serve as a supplementary energy conservation strategy. In the more saline metalimnion of ELB, an accumulation of inorganic nitrogen and phosphorus supports photosynthesis despite relatively low light levels. Conversely, in WLB the release of organic rich subglacial discharge from Taylor Glacier into WLB would be implicated in the possible high abundance of heterotrophs supported by increased potential for glycolysis, beta-oxidation, and glycoside hydrolase and may contribute to the growth of iron reducers in the dark and extremely saline hypolimnion of WLB. The suboxic and subzero temperature zones beneath the metalimnia in both lobes supported microorganisms capable of utilizing reduced nitrogens and sulfurs as electron donors. Heterotrophs, including nitrate reducing sulfur oxidizing bacteria, such as Acidimicrobiales (MAG72) and Salinisphaeraceae (MAG109), and denitrifying bacteria, such as Gracilimonas (MAG7), Acidimicrobiales (MAG72) and Salinisphaeraceae (MAG109), dominated the hypolimnion of WLB, whereas the environmental harshness of the hypolimnion of ELB was supported by the relatively low in metabolic potential, as well as the abundance of halophile Halomonas and endospore-forming Virgibacillus. Conclusions: The vertical distribution of microbially driven C, N and S cycling genes/pathways in Lake Bonney reveals the importance of geochemical gradients to microbial diversity and biogeochemical cycles with the vertical water column. [ABSTRACT FROM AUTHOR]

Simple Summary: Rodents, as the most abundant group of mammals, offer a unique opportunity to study the relationship between diet and host gut microecology. In this study, we focused on two species of the genus Myospalax in the Eurasian steppes in China: M. psilurus and M. aspalax. These specialized herbivorous rodents have adapted to a subterranean lifestyle and exhibit distinct dietary choices. Our study aimed to investigate how their diet composition is related to their gut microbial communities and whether there are unique indicator species for their gut microecology. Using 16S amplicon technology and macro-barcoding technology, we analyzed the gut bacterial communities and diet composition of the two zokor species. We found that M. psilurus had a higher diversity of gut microbial bacterial communities compared to M. aspalax. The two species also possessed different gut bacterial indicator species, with unique relationships between their diet and gut microbes. Our results provide new insights into the adaptation of zokors to long-term subterranean life and shed light on their cellulose degradation abilities and ecological niches. As the most abundant group of mammals, rodents possess a very rich ecotype, which makes them ideal for studying the relationship between diet and host gut microecology. Zokors are specialized herbivorous rodents adapted to living underground. Unlike more generalized herbivorous rodents, they feed on the underground parts of grassland plants. There are two species of the genus Myospalax in the Eurasian steppes in China: one is Myospalax psilurus, which inhabits meadow grasslands and forest edge areas, and the other is M. aspalax, which inhabits typical grassland areas. How are the dietary choices of the two species adapted to long-term subterranean life, and what is the relationship of this diet with gut microbes? Are there unique indicator genera for their gut microbial communities? Relevant factors, such as the ability of both species to degrade cellulose, are not yet clear. In this study, we analyzed the gut bacterial communities and diet compositions of two species of zokors using 16S amplicon technology combined with macro-barcoding technology. We found that the diversity of gut microbial bacterial communities in M. psilurus was significantly higher than that in M. aspalax, and that the two species of zokors possessed different gut bacterial indicator genera. Differences in the feeding habits of the two species of zokors stem from food composition rather than diversity. Based on the results of Mantel analyses, the gut bacterial community of M. aspalax showed a significant positive correlation with the creeping-rooted type food, and there was a complementary relationship between the axis root-type-food- and the rhizome-type-food-dominated (containing bulb types and tuberous root types) food groups. Functional prediction based on KEGG found that M. psilurus possessed a stronger degradation ability in the same cellulose degradation pathway. Neutral modeling results show that the gut flora of the M. psilurus has a wider ecological niche compared to that of the M. aspalax. This provides a new perspective for understanding how rodents living underground in grassland areas respond to changes in food conditions. [ABSTRACT FROM AUTHOR]

Huanglongbing, also known as citrus greening, is currently the most devastating citrus disease with limited success in prevention and mitigation. A promising strategy for Huanglongbing control is the use of antimicrobials fused to a carrier protein (phloem protein of 16 kDa or PP16) that targets vascular tissues. This study investigated the effects of genetically modified citrus trees expressing Citrus sinensis PP16 (CsPP16) fused to human lysozyme and β-defensin-2 on the soil microbiome diversity using 16S amplicon analysis. The results indicated that there were no significant alterations in alpha diversity, beta diversity, phylogenetic diversity, differential abundance, or functional prediction between the antimicrobial phloem-overexpressing plants and the control group, suggesting minimal impact on microbial community structure. However, microbiota diversity analysis revealed distinct bacterial assemblages between the rhizosphere soil and root environments. This study helps to understand the ecological implications of crops expressing phloem-targeted antimicrobials for vascular disease management, with minimal impact on soil microbiota. [ABSTRACT FROM AUTHOR]

Dolphins are aquatic mammals, whose role in microbial ecology is not fully understood. It is critical to study the microbiota of dolphins kept in captivity, as close contact with humans could unpredictably affect both human and animal health. In this study, we investigated the gut microbiota of 15 captive common bottlenose dolphins, and the relationship of microbial diversity and composition with animals’ age, sex, birthplace (dolphinarium or wildlife), and direct contacts with dolphinarium visitors using high-throughput V3-V4 16S rRNA amplicon sequencing. Based on acquired sequencing data we calculated and compared alpha and beta diversity indexes, as well as conducted differential abundance analysis of identified bacterial taxa to find multivariable associations with dolphins’ age period, sex, birthplace, and type of contact with humans with linear models. There was no association between gut microbiota composition and diversity and dolphins’ age period, sex, and birthplace. However, there were significant differences (q-value ≤ 0.00018) in the relative abundance of Edwardsiella genus in dolphins that were in contact only with dolphinarium staff in comparison to dolphins that apart from dolphinarium staff also had contact with dolphinarium visitors. These results show that dolphins born in wildlife and dolphinariums do not have significant differences in gut microbiota composition and the microbiota of captive dolphins can be affected by their contact with humans. [ABSTRACT FROM AUTHOR]

Background: Microbiomes are generally characterized by high diversity of coexisting microbial species and strains, and microbiome composition typically remains stable across a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. Therefore, the long-term persistence of microbiome diversity calls for an explanation. Results: To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis were obtained, namely, pure competition, host-parasite relationship, and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environment. Conclusions: The results of this modeling study show that basic phenomena that are universal in microbial communities, namely, environmental variation and HGT, provide for stabilization and persistence of microbial diversity, and emergence of ecological complexity. [ABSTRACT FROM AUTHOR]

Aim: To evaluate the root canal microbiome composition and bacterial functional capability in cases of primary and secondary apical periodontitis utilizing whole‐metagenome shotgun sequencing. Methodology: Twenty‐two samples from patients with primary root canal infections, and 18 samples obtained from previously treated teeth currently diagnosed with apical periodontitis were analysed with whole‐metagenome shotgun sequencing at a depth of 20 M reads. Taxonomic and functional gene annotations were made using MetaPhlAn3 and HUMAnN3 software. The Shannon and Chao1 indices were utilized to measure alpha diversity. Differences in community composition were evaluated utilizing analysis of similarity (ANOSIM) using Bray‐Curtis dissimilarities. The Wilcoxon rank sum test was used to compare differences in taxa and functional genes. Results: Microbial community variations within a community were significantly lower in secondary relative to primary infections (alpha diversity p =.001). Community composition was significantly different in primary versus secondary infection (R =.11, p =.005). The predominant taxa observed among samples (>2.5%) were Pseudopropionibacterium propionicum, Prevotella oris, Eubacterium infirmum, Tannerella forsythia, Atopobium rimae, Peptostreptococcus stomatis, Bacteroidetes bacterium oral taxon 272, Parvimonas micra, Olsenella profusa, Streptococcus anginosus, Lactobacillus rhamnosus, Porphyromonas endodontalis, Pseudoramibacter alactolyticus, Fusobacterium nucleatum, Eubacterium brachy and Solobacterium moorei. The Wilcoxon rank test revealed no significant differences in relative abundances of functional genes in both groups. Genes with greater relative abundances (top 25) were associated with genetic, signalling and cellular processes including the iron and peptide/nickel transport system. Numerous genes encoding toxins were identified: exfoliative toxin, haemolysins, thiol‐activated cytolysin, phospholipase C, cAMP factor, sialidase, and hyaluronic glucosaminidase. Conclusions: Despite taxonomic differences between primary and secondary apical periodontitis, the functional capability of the microbiomes was similar. [ABSTRACT FROM AUTHOR]

Abstract Background Gemmatimonadota bacteria are widely distributed in nature, but their metabolic potential and ecological roles in marine environments are poorly understood. Results Here, we obtained 495 metagenome-assembled genomes (MAGs), and associated viruses, from coastal to deep-sea sediments around the world. We used this expanded genomic catalog to compare the protein composition and update the phylogeny of these bacteria. The marine Gemmatimonadota are phylogenetically different from those previously reported from terrestrial environments. Functional analyses of these genomes revealed these marine genotypes are capable of degradation of complex organic carbon, denitrification, sulfate reduction, and oxidizing sulfide and sulfite. Interestingly, there is widespread genetic potential for secondary metabolite biosynthesis across Gemmatimonadota, which may represent an unexplored source of novel natural products. Furthermore, viruses associated with Gemmatimonadota have the potential to “hijack” and manipulate host metabolism, including the assembly of the lipopolysaccharide in their hosts. Conclusions This expanded genomic diversity advances our understanding of these globally distributed bacteria across a variety of ecosystems and reveals genetic distinctions between those in terrestrial and marine communities. Video Abstract

Outbreaks in Europe have raised concerns about poinsettia bacterial canker caused by Curtobacterium flaccumfaciens pv. poinsettiae, described in the United States. Using a semiselective medium containing aztreonam and fosfomycin and selection during isolation based on matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) spectra, 424 Curtobacterium strains were isolated from Belgian poinsettias of African and European origin. Different populations coexisted: 130 strains were identified as C. flaccumfaciens with scores ≥2.0 and 294 with scores

Abstract Background Antibiotic exposure can occur in medical settings and from environmental sources. Long-term effects of brief antibiotic exposure in early life are largely unknown. Results Post a short-term treatment by ceftriaxone to C57BL/6 mice in early life, a 14-month observation was performed using 16S rRNA gene-sequencing technique, metabolomics analysis, and metagenomics analysis on the effects of ceftriaxone exposure. Firstly, the results showed that antibiotic pre-treatment significantly disturbed gut microbial α and β diversities (P

Demand for natural gas continues to climb in the United States, having reached a record monthly high of 104.9 billion cubic feet per day (Bcf/d) in November 2023. Hydraulic fracturing, a technique used to extract natural gas and oil from deep underground reservoirs, involves injecting large volumes of fluid, proppant, and chemical additives into shale units. This is followed by a “shut-in” period, during which the fracture fluid remains pressurized in the well for several weeks. The microbial processes that occur within the reservoir during this shut-in period are not well understood; yet, these reactions may significantly impact the structural integrity and overall recovery of oil and gas from the well. To shed light on this critical phase, we conducted an analysis of both pre-shut-in material alongside production fluid collected throughout the initial production phase at the Hydraulic Fracturing Test Site 2 (HFTS 2) located in the prolific Wolfcamp formation within the Permian Delaware Basin of west Texas, USA. Specifically, we aimed to assess the microbial ecology and functional potential of the microbial community during this crucial time frame. Prior analysis of 16S rRNA sequencing data through the first 35 days of production revealed a strong selection for a Clostridia species corresponding to a significant decrease in microbial diversity. Here, we performed a metagenomic analysis of produced water sampled on Day 33 of production. This analysis yielded three highquality metagenome-assembled genomes (MAGs), one of which was a Clostridia draft genome closely related to the recently classified Petromonas tenebris. This draft genome likely represents the dominant Clostridia species observed in our 16S rRNA profile. Annotation of the MAGs revealed the presence of genes involved in critical metabolic processes, including thiosulfate reduction, mixed acid fermentation, and biofilm formation. These findings suggest that this microbial community has the potential to contribute to well souring, biocorrosion, and biofouling within the reservoir. Our research provides unique insights into the early stages of production in one of the most prolific unconventional plays in the United States, with important implications for well management and energy recovery. [ABSTRACT FROM AUTHOR]

Current knowledge about effects of disturbance on the fate of invaders in complex microbial ecosystems is still in its infancy. In order to investigate this issue, we compared the fate of Klebsiella pneumoniae (Kp) and Listeria monocytogenes (Lm) in soil microcosms. We then used environmental disturbances (freeze–thaw or heat cycles) to compare the fate of both invaders and manipulate soil microbial diversity. Population dynamics of the two pathogens was assessed over 50 days of invasion while microbial diversity was measured at times 0, 20 and 40 days. The outcome of invasion was strain-dependent and the response of the two invaders to disturbance differed. Resistance to Kp invasion was higher under the conditions where resident microbial diversity was the highest while a significant drop of diversity was linked to a higher persistence. In contrast, Lm faced stronger resistance to invasion in heat-treated microcosms where diversity was the lowest. Our results show that diversity is not a universal proxy of resistance to microbial invasion, indicating the need to properly assess other intrinsic properties of the invader, such as its metabolic repertoire, or the array of interactions between the invader and resident communities. [ABSTRACT FROM AUTHOR]

Microbial communities within oxygen minimum zones (OMZs) play crucial roles in the marine biogeochemical cycling. Arabian Sea (AS) has one of the largest OMZs among the global oceans, however, knowledge about the microbial ecology of the AS OMZ remained limited. In the present study, 44 water samples collected from six stations across the AS, spanning from the deep chlorophyll maximum (DCM) layer to 4000m depth were analyzed. High-throughput sequencing of 16S rRNA genes revealed the structural diversity of bacterial and archaeal communities, influenced primarily by depth and dissolved oxygen (DO) levels. Distinct community compositions were observed across different oxygen gradients, with shifts in the relative abundance of key taxa. Notably, Desulfosarcinaceae, UBA10353, Nitrospina, SUP05, Sva0996_marine_group, Microtrichaceae, and Nitrosopumilus emerged as bioindicator taxa in the AS hypoxic zones. Cooccurrence network analysis identified SAR324, Alteromonadaceae, and Sphingomonadaceae as keystone taxa. The spatial and depth-wise distribution patterns revealed that Desulfosarcinaceae was predominantly found in the hypoxic zones of the Arabian Sea, whereas UBA10353, Nitrospina, SUP05, Microtrichaceae and SAR324 were ubiquitous across AS, Bay of Bengal (BOB), and Eastern Tropical North Pacific (ETNP) OMZs, with OTU-level niche differentiation observed for the latter two. Functional profiling using FAPROTAX predicted higher metabolic potential for nitrogen and sulfur in the OMZ compared to other layers of the AS. Our findings provide valuable insights into the distribution, structure, and diversity of microbial communities in the AS OMZ, highlighting the ecological roles of key taxa in hypoxic environments. The established sequence database offers a foundation for further research into the complex interactions within these microbial ecosystems. [ABSTRACT FROM AUTHOR]

There is increasing evidence that interactions between microbes and their hosts not only play a role in determining health and disease but also in emotions, thought, and behavior. Built environments greatly influence microbiome exposures because of their built-in highly specific microbiomes coproduced with myriad metaorganisms including humans, pets, plants, rodents, and insects. Seemingly static built structures host complex ecologies of microorganisms that are only starting to be mapped. These microbial ecologies of built environments are directly and interdependently affected by social, spatial, and technological norms. Advances in technology have made these organisms visible and forced the scientific community and architects to rethink gene-environment and microbe interactions respectively. Thus, built environment design must consider the microbiome, and research involving host-microbiome interaction must consider the built-environment. This paradigm shift becomes increasingly important as evidence grows that contemporary built environments are steadily reducing the microbial diversity essential for human health, well-being, and resilience while accelerating the symptoms of human chronic diseases including environmental allergies, and other more life-altering diseases. New models of design are required to balance maximizing exposure to microbial diversity while minimizing exposure to human-associated diseases. Sustained trans-disciplinary research across time (evolutionary, historical, and generational) and space (cultural and geographical) is needed to develop experimental design protocols that address multigenerational multispecies health and health equity in built environments. [ABSTRACT FROM AUTHOR]

The composition and continuous succession of natural microbial communities during grape growth play important roles in grape health and flavor quality as well as in characterizing the regional wine terroir. This study explored the diversity and dynamics of fruit epidermal microbes at each growth and developmental stage of Ecolly grapes under an extremely simplified eco-cultivation model, analyzed microbial interactions and associations of weather parameters to specific communities, and emphasized metabolic functional characteristics of microecology. The results indicated that the natural microbial community changed significantly during the grape growth phase. The dominant fungal genera mainly included Gibberella, Alternaria, Filobasidium, Naganishia, Ascochyta, Apiotrichum, Comoclathris, and Aureobasidium, and the dominant bacterial genera mainly contained Sediminibacterium, Ralstonia, Pantoea, Bradyrhizobium, Brevundimonas, Mesorhizobium, Planococcus, and Planomicrobium. In summary, filamentous fungi gradually shifted to basidiomycetous yeasts along with fruit ripening, with a decline in the number of Gram-negative bacteria and a relative increase in Gram-positive bacteria. The community assembly process reflects the fact that microbial ecology may be influenced by a variety of factors, but the fungal community was more stable, and the bacterial community fluctuated more from year to year, which may reflect their response to weather conditions over the years. Overall, our study helps to comprehensively profile the ecological characteristics of the grape microbial system, highlights the natural ecological viticulture concept, and promotes the sustainable development of the grape and wine industry. [ABSTRACT FROM AUTHOR]

Background: Hot spring biofilms provide a window into the survival strategies of microbial communities in extreme environments and offer potential for biotechnological applications. This study focused on green and brown biofilms thriving on submerged plant litter within the Sungai Klah hot spring in Malaysia, characterised by temperatures of 58–74 °C. Using Illumina shotgun metagenomics and Nanopore ligation sequencing, we investigated the microbial diversity and functional potential of metagenome-assembled genomes (MAGs) with specific focus on biofilm formation, heat stress response, and carbohydrate catabolism. Results: Leveraging the power of both Illumina short-reads and Nanopore long-reads, we employed an Illumina-Nanopore hybrid assembly approach to construct MAGs with enhanced quality. The dereplication process, facilitated by the dRep tool, validated the efficiency of the hybrid assembly, yielding MAGs that reflected the intricate microbial diversity of these extreme ecosystems. The comprehensive analysis of these MAGs uncovered intriguing insights into the survival strategies of thermophilic taxa in the hot spring biofilms. Moreover, we examined the plant litter degradation potential within the biofilms, shedding light on the participation of diverse microbial taxa in the breakdown of starch, cellulose, and hemicellulose. We highlight that Chloroflexota and Armatimonadota MAGs exhibited a wide array of glycosyl hydrolases targeting various carbohydrate substrates, underscoring their metabolic versatility in utilisation of carbohydrates at elevated temperatures. Conclusions: This study advances understanding of microbial ecology on plant litter under elevated temperature by revealing the functional adaptation of MAGs from hot spring biofilms. In addition, our findings highlight potential for biotechnology application through identification of thermophilic lignocellulose-degrading enzymes. By demonstrating the efficiency of hybrid assembly utilising Illumina-Nanopore reads, we highlight the value of combining multiple sequencing methods for a more thorough exploration of complex microbial communities. [ABSTRACT FROM AUTHOR]

Mangroves are important coastal wetlands along tropical and subtropical regions. Pneumatophore, a kind of aerial root, is among the prominent components of a mangrove ecosystem, which provides microhabitats for a range of prokaryotic (bacteria and cyanobacteria) microbial assemblages, whose role in the maintenance of mangrove ecology often remains neglected. Very few studies are available on pneumatophore-associated prokaryotic microorganisms (PAPMs). The majority of them are related to the microscopic identification of cyanobacteria, with very limited research on the bacterial population, even though they demand more attention. Also, very scarce information is available on biotic and abiotic factors shaping the PAPMs. The objective of this review is to highlight the structural and functional importance of prokaryotic organisms associated with pneumatophores. This review begins with a brief introduction of what mangrove pneumatophores are, then focuses on the PAPMs, accentuating the breadth and depth of information gained from previous research. We further discuss how a combination of a traditional cultivable approach and a newly developed omics approach can be efficaciously employed to untangle PAPMs. This review provides updated information on PAPMs, which will intensify the visibility and necessity of pneumatophore-associated microbial community research. [ABSTRACT FROM AUTHOR]

Understanding the intricate ecological interactions within the gut microbiome and unravelling its impact on human health is a challenging task. Bioreactors are valuable tools that have contributed to our understanding of gut microbial ecology. However, there is a lack of studies describing and comparing the microbial diversity cultivated in these models. This knowledge is crucial for refining current models to reflect the gastrointestinal microbiome accurately. In this study, we analysed the microbial diversity of 1512 samples from 18 studies available in public repositories that employed cultures performed in batches and various bioreactor models to cultivate faecal microbiota. Community structure comparison between samples using t-distributed stochastic neighbour embedding and the Hellinger distance revealed a high variation between projects. The main driver of these differences was the inter-individual variation between the donor faecal inocula. Moreover, there was no overlap in the structure of the microbial communities between studies using the same bioreactor platform. In addition, α-diversity analysis using Hill numbers showed that highly complex bioreactors did not exhibit higher diversities than simpler designs. However, analyses of five projects in which the samples from the faecal inoculum were also provided revealed an amplicon sequence variants enrichment in bioreactors compared to the inoculum. Finally, a comparative analysis of the taxonomy of the families detected in the projects and the GMRepo database revealed bacterial families exclusively found in the bioreactor models. These findings highlight the potential of bioreactors to enrich low-abundance microorganisms from faecal samples, contributing to uncovering the gut microbial "dark matter". [ABSTRACT FROM AUTHOR]

Abstract Background Antarctica and its unique biodiversity are increasingly at risk from the effects of global climate change and other human influences. A significant recent element underpinning strategies for Antarctic conservation has been the development of a system of Antarctic Conservation Biogeographic Regions (ACBRs). The datasets supporting this classification are, however, dominated by eukaryotic taxa, with contributions from the bacterial domain restricted to Actinomycetota and Cyanobacteriota. Nevertheless, the ice-free areas of the Antarctic continent and the sub-Antarctic islands are dominated in terms of diversity by bacteria. Our study aims to generate a comprehensive phylogenetic dataset of Antarctic bacteria with wide geographical coverage on the continent and sub-Antarctic islands, to investigate whether bacterial diversity and distribution is reflected in the current ACBRs. Results Soil bacterial diversity and community composition did not fully conform with the ACBR classification. Although 19% of the variability was explained by this classification, the largest differences in bacterial community composition were between the broader continental and maritime Antarctic regions, where a degree of structural overlapping within continental and maritime bacterial communities was apparent, not fully reflecting the division into separate ACBRs. Strong divergence in soil bacterial community composition was also apparent between the Antarctic/sub-Antarctic islands and the Antarctic mainland. Bacterial communities were partially shaped by bioclimatic conditions, with 28% of dominant genera showing habitat preferences connected to at least one of the bioclimatic variables included in our analyses. These genera were also reported as indicator taxa for the ACBRs. Conclusions Overall, our data indicate that the current ACBR subdivision of the Antarctic continent does not fully reflect bacterial distribution and diversity in Antarctica. We observed considerable overlap in the structure of soil bacterial communities within the maritime Antarctic region and within the continental Antarctic region. Our results also suggest that bacterial communities might be impacted by regional climatic and other environmental changes. The dataset developed in this study provides a comprehensive baseline that will provide a valuable tool for biodiversity conservation efforts on the continent. Further studies are clearly required, and we emphasize the need for more extensive campaigns to systematically sample and characterize Antarctic and sub-Antarctic soil microbial communities. Video Abstract

Acidic salt lakes are environments that harbor an array of biologically challenging conditions. Through 16S rRNA, 18S rRNA, and ITS amplicon sequencing of eight such lakes across the Yilgarn Craton of Western Australia, we aim to understand the microbial ecology of these lakes with a focus on iron- and sulfur-oxidizing and reducing microorganisms that have theoretical application in biomining industries. In spite of the biological challenges to life in these lakes, the microbial communities were highly diverse. Redundancy analysis of soil samples revealed sulfur, ammonium, organic carbon, and potassium were significant diversities of the microbial community composition. The most abundant microbes with a hypothetical application in biomining include the genus 9  M32 of the Acidithiobacillus family, Alicyclobacillus and Acidiphilium, all of which are possible iron- and/or sulfur-oxidizing bacteria. It is evident through this study that these lakes harbor multiple organisms with potential in biomining industries that should be exploited and studied further. [ABSTRACT FROM AUTHOR]

Understanding the relation between terrestrial microorganisms and edaphic factors in the Antarctic can provide insights into their potential response to environmental changes. Here we examined the composition of bacterial and micro-eukaryotic communities using amplicon sequencing of rRNA genes in 105 soil samples from the Sør Rondane Mountains (East Antarctica), differing in bedrock or substrate type and associated physicochemical conditions. Although the two most widespread taxa (Acidobacteriota and Chlorophyta) were relatively abundant in each sample, multivariate analysis and co-occurrence networks revealed pronounced differences in community structure depending on substrate type. In moraine substrates, Actinomycetota and Cercozoa were the most abundant bacterial and eukaryotic phyla, whereas on gneiss, granite and marble substrates, Cyanobacteriota and Metazoa were the dominant bacterial and eukaryotic taxa. However, at lower taxonomic level, a distinct differentiation was observed within the Cyanobacteriota phylum depending on substrate type, with granite being dominated by the Nostocaceae family and marble by the Chroococcidiopsaceae family. Surprisingly, metazoans were relatively abundant according to the 18S rRNA dataset, even in samples from the most arid sites, such as moraines in Austkampane and Widerøefjellet ("Dry Valley"). Overall, our study shows that different substrate types support distinct microbial communities, and that mineral soil diversity is a major determinant of terrestrial microbial diversity in inland Antarctic nunataks and valleys. [ABSTRACT FROM AUTHOR]

Hydrocarbon pollution is a major ecological problem facing oil-producing countries, especially in the Niger Delta region of Nigeria. In this study, a site that had been previously polluted by artisanal refining activity was investigated using 16S rRNA Illumina high-throughput sequencing technology and bioinformatics tools. These were used to investigate the bacterial diversity in soil with varying degrees of contamination, determined with a gas chromatography-flame ionization detector (GC-FID). Soil samples were collected from a heavily polluted (HP), mildly polluted (MP), and unpolluted (control sample, CS) portion of the study site. DNA was extracted using the Zymo Research (ZR) Fungi/Bacteria DNA MiniPrep kit, followed by PCR amplification and agarose gel electrophoresis. The microbiome was characterized based on the V3 and V4 hypervariable regions of the 16S rRNA gene. QIIME (Quantitative Insights Into Microbial Ecology) 2 software was used to analyse the sequence data. The final data set covered 20,640 demultiplexed high-quality reads and a total of 160 filtered bacterial OTUs. Proteobacteria dominated samples HP and CS, while Actinobacteria dominated sample MP. Denitratisoma, Pseudorhodoplanes, and Spirilospora were the leading genera in samples HP, CS, and MP respectively. Diversity analysis indicated that CS [with 25.98 ppm of total petroleum hydrocarbon (TPH)] is more diverse than HP (with 490,630 ppm of TPH) and MP (with 5398 ppm of TPH). A functional prediction study revealed that six functional modules dominated the dataset, with metabolism covering up to 70%, and 11 metabolic pathways. This study demonstrates that a higher hydrocarbon concentration in soil adversely impacts microbial diversity, creating a narrow bacterial diversity dominated by hydrocarbon-degrading species, in addition to the obvious land and ecosystem degradation caused by artisanal refining activities. Overall, the artisanal refining business is significantly driving ecosystem services losses in the Niger Delta, which calls for urgent intervention, with focus on bioremediation. [ABSTRACT FROM AUTHOR]

Micritization is an early diagenetic process that gradually alters primary carbonate sediment grains through cycles of dissolution and reprecipitation of microcrystalline calcite (micrite). Typically observed in modern shallow marine environments, micritic textures have been recognized as a vital component of storage and flow in hydrocarbon reservoirs, attracting scientific and economic interests. Due to their endolithic activity and the ability to promote nucleation and reprecipitation of carbonate crystals, microorganisms have progressively been shown to be key players in micritization, placing this process at the boundary between the geological and biological realms. However, published research is mainly based on geological and geochemical perspectives, overlooking the biological and ecological complexity of microbial communities of micritized sediments. In this paper, we summarize the state‐of‐the‐art and research gaps in micritization from a microbial ecology perspective. Since a growing body of literature successfully applies in vitro and in situ 'fishing' strategies to unveil elusive microorganisms and expand our knowledge of microbial diversity, we encourage their application to the study of micritization. By employing these strategies in micritization research, we advocate promoting an interdisciplinary approach/perspective to identify and understand the overlooked/neglected microbial players and key pathways governing this phenomenon and their ecology/dynamics, reshaping our comprehension of this process. [ABSTRACT FROM AUTHOR]

The Barents Sea shelf is one of the most economically promising regions in the Arctic in terms of its resources and geographic location. However, benthic microbial communities of the northeastern Barents Sea are still barely studied. Here, we present a detailed systematic description of the structures of microbial communities located in the sediments and bottom water of the northeastern Barents Sea based on 16S rRNA profiling and a qPCR assessment of the total prokaryotic abundance in 177 samples. Beta- and alpha-diversity analyses revealed a clear difference between the microbial communities of diverse sediment layers and bottom-water fractions. We identified 101 microbial taxa whose representatives had statistically reliable distribution patterns between these ecotopes. Analysis of the correlation between microbial community structure and geological data yielded a number of important results—correlations were found between the abundance of individual microbial taxa and bottom relief, thickness of marine sediments, presence of hydrotrolite interlayers, and the values of pH and Eh. We also demonstrated that a relatively high abundance of prokaryotes in sediments can be caused by the proliferation of Deltaproteobacteria representatives, in particular, sulfate and iron reducers. [ABSTRACT FROM AUTHOR]

Background: Pakistan is a multi-ethnic society where there is a disparity between dietary habits, genetic composition, and environmental exposures. The microbial ecology of healthy Pakistani gut in the context of anthropometric, sociodemographic, and dietary patterns holds interest by virtue of it being one of the most populous countries, and also being a Lower Middle Income Country (LMIC). Methods: 16S rRNA profiling of healthy gut microbiome of normo-weight healthy Pakistani individuals from different regions of residence is performed with additional meta-data collected through filled questionnaires. The current health status is then linked to dietary patterns through χ 2 test of independence and Generalized Linear Latent Variable Model (GLLVM) where distribution of individual microbes is regressed against all recorded sources of variability. To identify the core microbiome signature, a dynamic approach is used that considers into account species occupancy as well as consistency across assumed grouping of samples including organization by gender and province of residence. Fitting neutral modeling then revealed core microbiome that is selected by the environment. Results: A strong determinant of disparity is by province of residence. It is also established that the male microbiome is better adapted to the local niche than the female microbiome, and that there is microbial taxonomic and functional diversity in different ethnicities, dietary patterns and lifestyle habits. Some microbial genera, such as, Megamonas, Porphyromonas, Haemophilus, Klebsiella and Finegoldia showed significant associations with consumption of pickle, fresh fruits, rice, and cheese. Our analyses suggest current health status being associated with the diet, sleeping patterns, employment status, and the medical history. Conclusions: This study provides a snapshot of the healthy core Pakistani gut microbiome by focusing on the most populous provinces and ethnic groups residing in predominantly urban areas. The study serves a reference dataset for exploring variations in disease status and designing personalized dietary and lifestyle interventions to promote gut health, particularly in LMICs settings. [ABSTRACT FROM AUTHOR]

Spatial heterogeneity significantly enhances biodiversity, representing one of the ecology's most enduring paradigms. However, many studies have found decreasing, humped, and neutral correlations between spatial heterogeneity and biodiversity (heterogeneity–diversity relationships, HDR). These findings have pushed this widely accepted theory back into controversy. Microbial HDR research has lagged compared to that of plants and animals. Nevertheless, microbes have features that add a temporal-scale perspective to HDR research that is critical to understanding patterns of HDR. In this study, 157 microcosms with different types spatial heterogeneity were set up to map the HDR of microorganisms and their temporal dynamics using high-throughput sequencing techniques. The results show that the following: 1. Spatial heterogeneity can significantly alter microbial diversity in microcosmic systems. Changes in microbial diversity, in turn, lead to changes in environmental conditions. These changes caused microorganisms to exhibit increasing, decreasing, humped, U-shaped, and neutral HDR patterns. 2. The emergence of HDR patterns is characterized by temporal dynamics. Additionally, the HDR patterns generated by spatial structural and compositional heterogeneity exhibit inconsistent emergence times. These results suggest that the temporal dynamics of HDR may be one of the reasons for the coexistence of multiple patterns in previous studies. The feedback regulation between spatial heterogeneity–biodiversity–environmental conditions is an essential reason for the temporally dynamics of HDR patterns. All future ecological studies should pay attention to the temporal dynamic patterns of ecological factors. [ABSTRACT FROM AUTHOR]

Understanding the processes that underpin the community assembly of bacteria is a key challenge in microbial ecology. We studied soil bacterial communities across a large‐scale successional gradient of managed and abandoned grasslands paired with mature forest sites to disentangle drivers of community turnover and assembly. Diversity partitioning and phylogenetic null‐modelling showed that bacterial communities in grasslands remain compositionally stable following abandonment and secondary succession but they differ markedly from fully afforested sites. Zeta diversity analyses revealed the persistence of core microbial taxa that both reflected and differed from whole‐scale community turnover patterns. Differences in soil pH and C:N were the main drivers of community turnover between paired grassland and forest sites and the variability of pH within successional stages was a key factor related to the relative dominance of deterministic assembly processes. Our results indicate that grassland microbiomes could be compositionally resilient to abandonment and secondary succession and that the major changes in microbial communities between grasslands and forests occur fairly late in the succession when trees have established as the dominant vegetation. We also show that core taxa may show contrasting responses to management and abandonment in grasslands. [ABSTRACT FROM AUTHOR]

This document discusses the diversity and dynamics of microbial communities in marine ecosystems. Microbes play a crucial role in marine ecosystems, contributing to biogeochemical cycles and nutrient cycling. These communities adapt to different conditions and undergo dynamic shifts influenced by factors like temperature and nutrient availability. Advances in DNA sequencing have allowed researchers to study these communities in greater detail. The document includes specific studies on bacterial communities in sea cucumber culture ponds, the abundance and community structure of Labyrinthulomycetes in the South China Sea, the variability of phytoplankton structure in the Qinhuangdao coastal area, the impact of typhoons on microbial communities and water quality, the prevalence of antibiotic-resistant E. coli in an urban coastal beach, the dynamics of microbial communities and carbon sequestration in coastal ecosystems, and the diversity and community composition of Labyrinthulomycetes in the coastal zone of Hainan Island. These studies provide valuable insights into the complexity and importance of microbial communities in marine ecosystems. [Extracted from the article]

Few studies have been reported on the effect of planting years on fruit quality and soil of pear trees. In this study, four planting years (T5, T20, T30, and T40) of Cuiguan pears were used to analyze fruit quality, rhizosphere soil enzymes, and microbial diversity of pear trees, and their correlations. The results showed that the content of sucrose, reducing sugar and ascorbic acid in Cuiguan Pear showed a tendency of increasing and then decreasing with the increase of planting years, in which the highest content was found in 20- and 30-year-old fruits, and the highest content of total acid was found in 5-year-old fruits. Rhizosphere soil enzyme activities varied with planting year, with the highest protease activity in 20-year-old soil, phosphatase and urease in 30-year-old soil, polyphenol oxidase in 5-year-old soil, and sucrase in 40-year-old soil. The microbial diversity index and the number of OTUs showed an increasing and decreasing trend with the increase of planting years. Among the top 11 bacteria in pear rhizosphere soil average relative abundance, with Bradyrhizobium decreasing in relative abundance at the peak pear fruiting stages (T20 and T30), while Acidothermus showed an increasing trend in relative abundance with increasing planting years. RDA analysis showed that there were differences in the microbial community structure of pear trees at different planting years, and that both sucrose and reducing sugar contents in pears were positively correlated with T20 and T30, ascorbic acid content was positively correlated with T40, whereas the total acid content was positively correlated with T5, and that T20 was positively correlated with soil protease and phosphate mono esterase activities, and that T30 was positively correlated with polyphenol oxidase and urease activities, whereas T40 was positively correlated with sucrase activity. In summary, with the increase of planting years, changes in soil microbial community structure and soil enzyme activity have a significant impact on pear quality formation, and the results of the study provide a theoretical basis for scientific management of pear orchards.

This document is an editorial published in the journal Frontiers in Plant Science. It discusses the importance of plant-microbe interactions in forest ecosystems. Forests play a crucial role in preserving biodiversity and mitigating climate change by sequestering carbon dioxide. Microorganisms in forest soils are responsible for nutrient cycling and form symbiotic relationships with forest species. Understanding these interactions is essential for effective forest management. The editorial also highlights specific research articles that explore the diversity of fungi associated with tree diseases, the influence of mycorrhizal fungi on microbial communities and litter decomposition, and the role of soil microorganisms in seed germination. The document emphasizes the need to consider microbiota in the management of ecosystems and encourages further research in this field. [Extracted from the article]

A variety of microorganisms grow in oil reservoirs, where they participate in the biodegradation of oil and lead to changes in oil quality. Today, our knowledge about microbial processes in oil reservoirs is largely limited, and among the urgent tasks for the oil industry, monitoring and controlling microbial activity (including the activity of microbes responsible for biocorrosion) are important. In this work, we aimed to characterize the bacterial community structure of the produced waters from oilfields in the south of the Republic of Tatarstan (Russian Federation) using cultural and molecular methods of analysis. Bacteria from produced water samples from various oil wells were enriched, and 16S rRNA gene amplicon sequencing was used to assess the phylogenetic diversity of the bacterial communities. Thus, analysis of the bacterial communities revealed the presence of various members within the genera Desulfotomaculum, Clostridium, Acetobacterium, Desulfovibrio, Dethiosulfovibrio, Desulfomicrobium, Fusibacter, Dethiosulfatibacter, Thermovirga, Sphaerochaeta, and Desulfoplanes, but in different produced water samples. The role of the bacterial associations in biocorrosion was separately assessed in experiments on monitoring and stimulating biocorrosion. The bacterial community receiving additional nutrition was shown to have a higher corrosion potential, and scanning electron microscopy analysis confirmed changes in the surface of the metal coupons during immersion testing. The practical value of this research lies in identifying the potential contribution of microbial communities to oil pipeline corrosion. [ABSTRACT FROM AUTHOR]

Massive quantitities of waste generated by rising human population and rapid urbanisation are often disposed of into open dumps or landfills. The leachates released from these dumpsites penetrate the soil and can alter the existing biotic communities of the soil. In soil, the microbial communities are the dominant drivers which undergo changes in community structure and diversity in response to the changes in their biotic and abiotic environment. The heterogeneous waste disposed in a dumpsite or a landfill releases leachate containing nutrients along with toxic chemicals and allochthonous microorganisms in the soil. How the microbial community structure and diversity changes in a landfill or a dumpsite soil receiving leachate from it are some important questions from the perspective of microbial ecology. To unravel the community structure of bacteria inthe soil receiving dumpsite leachate and to assess the disturbance diversity relationship in this site, a comparative metagenomic analysis of the soil receiving dumpsite leachate and that of the soil of an adjacent wetland (conserved under Ramsar convention) not receiving dumpsite leachate used as the reference point was done to observe the effect of waste dumping activity on microbial diversity. The microbial diversity of the soil receiving dumpsite leachate and that of the wetland soil were found to differ significantly. Higher microbial diversity was observed in the dumpsite soil, while the wetland soil showed relative dominance of a few microbial taxa. [ABSTRACT FROM AUTHOR]

1‐Kestose (KES), a dietary fiber and prebiotic carbohydrate, benefits various physiological functions. This study aimed to examine whether diets supplemented with KES over three consecutive generations could significantly affect some host physiological aspects, including behavioral phenotypes and gut microbial ecology. Mice that received KES‐supplemented diets for three generations demonstrated increased activity compared with those fed diets lacking KES. Furthermore, the KES group showed increased striatal dopamine (DA) and serotonin (5‐HT) levels. The observed increase in DA levels within the striatum was positively correlated with locomotor activity in the KES group but not in the control (CON) group. The α‐diversities were significantly lower in the KES group compared to the CON group. The three‐dimensional principal coordinate analysis revealed a substantial distinction between the KES and CON groups across each generation. At the genus level, most gut microbiota genera exhibited lower abundances in the KES group than in the CON group, except for Bifidobacteria and Akkermansia. Spearman's rank‐order analysis indicated significant negative correlations between the striatal DA levels and α‐diversity values. These findings suggest that prolonged supplementation with KES may stimulate increased locomotor activity along with elevated striatal DA levels, which are potentially associated with KES‐induced alterations in the gut microbiota. [ABSTRACT FROM AUTHOR]

Background and Objectives: Rinaie Marwah hot spring Kishtwar (RMHSK) is one of the geothermal springs located at 33°51'51"N 75°32'07"E with an elevation of 2134 meters above sea level in Jammu and Kashmir, India. We aimed to study the microbial diversity of this geothermal spring using metagenomics. Materials and Methods: In the present study, physiochemical parameters including temperature (65-75oC), pH (6. 9-8. 8), hardness (250 ppm), and mineral content was measured along with the microbial diversity using Illumina MiSeq metagenome-based 16s amplicon sequencing (V3-V4). The sequence reads were classified taxonomically into 31 phyla, 71 classes, 152 orders, 256 families, 410 genus, and 665 species. QIIME 2 (Quantitative Insights into Microbial Ecology), an extensible, powerful, and decentralized analytical tool, was used for taxonomic analysis. Results: Bacteroidota (32. 57%) was the dominant phylum, Bacteroidia (32. 51%) the dominant class, Bacteroidales (16. 6%) the dominant order, and Lentimicrobiaceae (14. 23%) was the dominant family per the abundance analysis. Shannon (2. 28) and Chao 1 (87. 0) diversity indices support the existence of higher microbial diversity in RMHSK (50717 OTUs). Conclusion: The microbial diversity of RMHSK is reported for the first time through a metagenomic study. Identification of microorganisms with characteristics that are relevant to industries. [ABSTRACT FROM AUTHOR]

Background The health index of any population is directly correlated with the water quality, which in turn depends upon physicochemical characteristics and the microbiome of that aquatic source. For maintaining the water quality, knowledge of microbial diversity is a must. The present investigation attempts to evaluate the microflora of Baner. Metagenomics has been proven to be the technique for examining the genetic diversity of unculturable microbiota without using traditional culturing techniques. The microbial profile of Baner is analyzed using metagenomics for the first time to the best of our knowledge. Results To explore the microbial diversity of Baner, metagenomics analysis from 3 different sites was done. Data analysis identified 29 phyla, 62 classes, 131 orders, 268 families, and 741 genera. Proteobacteria was found to be the most abundant phylum in all the sampling sites, with the highest abundance at S3 sampling site (94%). Bacteroidetes phylum was found to be second abundant in S1 and S2 site, whereas Actinobacteria was second dominant in sampling site S3. Enterobacteriaceae family was dominant in site S1, whereas Comamonadaceae and Pseudomonadaceae was abundant in sites S2 and S3 respectively. The Baner possesses an abundant bacterial profile that holds great promise for developing bioremediation tactics against a variety of harmful substances. Conclusion Baner river's metagenomic analysis offers the first insight into the microbial profile of this hilly stream. Proteobacteria was found to be the most abundant phylum in all the sampling sites indicating anthropogenic interference and sewage contamination. The highest abundance of proteobacteria at S3 reveals it to be the most polluted site, as it is the last sampling site downstream of the area under investigation, and falls after crossing the main city, so more human intervention and pollution were observed. Despite some pathogens, a rich profile of bacteria involved in bioremediation, xenobiotic degradation, and beneficial fish probiotics was observed, reflecting their potential applications for improving water quality and establishing a healthy aquaculture and fishery section. [ABSTRACT FROM AUTHOR]

Over the years, microbial community composition in the rhizosphere has been extensively studied as the most fascinating topic in microbial ecology. In general, plants affect soil microbiota through rhizodeposits and changes in abiotic conditions. However, a consensus on the response of microbiota traits to the rhizosphere and bulk soils in various ecosystems worldwide regarding community diversity and structure has not been reached yet. Here, we conducted a meta-analysis of 101 studies to investigate the microbial community changes between the rhizosphere and bulk soils across various plant species (maize, rice, vegetables, other crops, herbaceous, and woody plants). Our results showed that across all plant species, plant rhizosphere effects tended to reduce the rhizosphere soil pH, especially in neutral or slightly alkaline soils. Beta-diversity of bacterial community was significantly separated between into rhizosphere and bulk soils. Moreover, r-strategists and copiotrophs (e.g. Proteobacteria and Bacteroidetes) enriched by 24-27% in the rhizosphere across all plant species, while K-strategists and oligotrophic (e.g. Acidobacteria, Gemmatimonadete, Nitrospirae, and Planctomycetes) decreased by 15-42% in the rhizosphere. Actinobacteria, Firmicutes, and Chloroflexi are also depleted by in the plant rhizosphere compared with the bulk soil by 7-14%. The Actinobacteria exhibited consistently negative effect sizes across all plant species, except for maize and vegetables. In Firmicutes, both herbaceous and woody plants showed negative responses to rhizosphere effects, but those in maize and rice were contrarily enriched in the rhizosphere. With regards to Chloroflexi, apart from herbaceous plants showing a positive effect size, the plant rhizosphere effects were consistently negative across all other plant types. Verrucomicrobia exhibited a significantly positive effect size in maize, whereas herbaceous plants displayed a negative effect size in the rhizosphere. Overall, our meta-analysis exhibited significant changes in microbial community structure and diversity responding to the plant rhizosphere effects depending on plant species, further suggesting the importance of plant rhizosphere to environmental changes influencing plants and subsequently their controls over the rhizosphere microbiota related to nutrient cycling and soil health. [ABSTRACT FROM AUTHOR]

Real-time quantitative PCR (qPCR) has been widely used to quantify gene copy numbers in microbial ecology. Despite its simplicity and straightforwardness, establishing qPCR assays is often impeded by the tedious process of producing qPCR standards by cloning the target DNA into plasmids. Here, we designed double-stranded synthetic DNA fragments from consensus sequences as qPCR standards by aligning microbial gene sequences (10-20 sequences per gene). Efficiency of standards from synthetic DNA was compared with plasmid standards by qPCR assays for different phylogenetic marker and functional genes involved in carbon (C) and nitrogen (N) cycling, tested with DNA extracted from a broad range of soils. Results showed that qPCR standard curves using synthetic DNA performed equally well to those from plasmids for all the genes tested. Furthermore, gene copy numbers from DNA extracted from soils obtained by using synthetic standards or plasmid standards were comparable. Our approach therefore demonstrates that a synthetic DNA fragment as qPCR standard provides comparable sensitivity and reliability to a traditional plasmid standard, while being more time- and cost-efficient. [ABSTRACT FROM AUTHOR]

Background: The use of omics data for monitoring the microbial flow of fresh meat products along a production line and the development of spoilage prediction tools from these data is a promising but challenging task. In this context, we produced a large multivariate dataset (over 600 samples) obtained on the production lines of two similar types of fresh meat products (poultry and raw pork sausages). We describe a full analysis of this dataset in order to decipher how the spoilage microbial ecology of these two similar products may be shaped differently depending on production parameter characteristics. Methods: Our strategy involved a holistic approach to integrate unsupervised and supervised statistical methods on multivariate data (OTU-based microbial diversity; metabolomic data of volatile organic compounds; sensory measurements; growth parameters), and a specific selection of potential uncontrolled (initial microbiota composition) or controlled (packaging type; lactate concentration) drivers. Results: Our results demonstrate that the initial microbiota, which is shown to be very different between poultry and pork sausages, has a major impact on the spoilage scenarios and on the effect that a downstream parameter such as packaging type has on the overall evolution of the microbial community. Depending on the process, we also show that specific actions on the pork meat (such as deboning and defatting) elicit specific food spoilers such as Dellaglioa algida, which becomes dominant during storage. Finally, ecological network reconstruction allowed us to map six different metabolic pathways involved in the production of volatile organic compounds involved in spoilage. We were able connect them to the different bacterial actors and to the influence of packaging type in an overall view. For instance, our results demonstrate a new role of Vibrionaceae in isopropanol production, and of Latilactobacillus fuchuensis and Lactococcus piscium in methanethiol/disylphide production. We also highlight a possible commensal behavior between Leuconostoc carnosum and Latilactobacillus curvatus around 2,3-butanediol metabolism. Conclusion: We conclude that our holistic approach combined with largescale multi-omic data was a powerful strategy to prioritize the role of production parameters, already known in the literature, that shape the evolution and/or the implementation of different meat spoilage scenarios. [ABSTRACT FROM AUTHOR]

Introduction: The impact of plastics on terrestrial ecosystems is receiving increasing attention. Although of great importance to soil biogeochemical processes, how plastics influence soil microbes have yet to be systematically studied. The primary objectives of this study are to evaluate whether plastics lead to divergent responses of soil microbial community parameters, and explore the potential driving factors. Methods: We performed a meta-analysis of 710 paired observations from 48 published articles to quantify the impact of plastic on the diversity, biomass, and functionality of soil microbial communities. Results and discussion: This study indicated that plastics accelerated soil organic carbon loss (effect size = -0.05, p = 0.004) and increased microbial functionality (effect size = 0.04, p = 0.003), but also reduced microbial biomass (effect size = -0.07, p< 0.001) and the stability of co-occurrence networks. Polyethylene significantly reduced microbial richness (effect size = -0.07, p< 0.001) while polypropylene significantly increased it (effect size = 0.17, p < 0.001). Degradable plastics always had an insignificant effect on the microbial community. The effect of the plastic amount on microbial functionality followed the "hormetic dose-response" model, the infection point was about 40g/kg. Approximately 3564.78 pm was the size of the plastic at which the response of microbial functionality changed from positive to negative. Changes in soil pH, soil organic carbon, and total nitrogen were significantly positively correlated with soil microbial functionality, biomass, and richness (R² = 0.04-0.73, p < 0.05). The changes in microbial diversity were decoupled from microbial community structure and functionality. We emphasize the negative impacts of plastics on soil microbial communities such as microbial abundance, essential to reducing the risk of ecological surprise in terrestrial ecosystems. Our comprehensive assessment of plastics on soil microbial community parameters deepens the understanding of environmental impacts and ecological risks from this emerging pollution. [ABSTRACT FROM AUTHOR]

The horizontal transfer of genes is fundamental for the eco-evolutionary dynamics of microbial communities, such as oceanic plankton, soil, and the human microbiome. In the case of an acquired beneficial gene, classic population genetics would predict a genome-wide selective sweep, whereby the genome spreads clonally within the community and together with the beneficial gene, removing genome diversity. Instead, several sources of metagenomic data show the existence of "gene-specific sweeps", whereby a beneficial gene spreads across a bacterial community, maintaining genome diversity. Several hypotheses have been proposed to explain this process, including the decreasing gene flow between ecologically distant populations, frequency-dependent selection from linked deleterious allelles, and very high rates of horizontal gene transfer. Here, we propose an additional possible scenario grounded in eco-evolutionary principles. Specifically, we show by a mathematical model and simulations that a metacommunity where species can occupy multiple patches, acting together with a realistic (moderate) HGT rate, helps maintain genome diversity. Assuming a scenario of patches dominated by single species, our model predicts that diversity only decreases moderately upon the arrival of a new beneficial gene, and that losses in diversity can be quickly restored. We explore the generic behaviour of diversity as a function of three key parameters, frequency of insertion of new beneficial genes, migration rates and horizontal transfer rates.Our results provides a testable explanation for how diversity can be maintained by gene-specific sweeps even in the absence of high horizontal gene transfer rates. Author summary: Our study investigates the interactions between gene-specific selective sweeps, horizontal gene transfer (HGT), and genome diversity within microbial communities. Using mathematical models and simulations, we examine the time scales involved in these processes to gain insights into their complex dynamics. Our findings highlight the importance of considering both HGT and metacommunity structure. Contrary to previous assumptions that gene-specific selective sweeps lead to a decrease in biodiversity, we find that genome diversity can be regenerated under moderate rates of HGT. Our results offer a verifiable explanation for the preservation of diversity in the presence of gene-specific sweeps, even when high rates of horizontal gene transfer are absent. [ABSTRACT FROM AUTHOR]

River and reservoir bacterial communities are the most basic part of river biomes and ecosystem structure, and play an important role in river biological processes. Yet, it remains unclear how highly regulated dam reservoirs affect both soil and sediment bacterial communities. A temporal distribution pattern of bacterial communities was investigated using Illumina MiSeq sequencing in a transition section of the Three Gorges Reservoir (TGR). In total, 106,682 features belong to the bacteria kingdom, encompassing 95 phyla, 228 classes, 514 orders, 871 families, 1959 genera, and 3,053 species. With water level regulation, Shannon diversity index, and observed species differed significantly, with no significant difference in Simpson evenness. Both in the high water level period (October) and the low water level period (June), Proteobacteria, Acidobacteri, and Chloroflexi were the most abundant phyla. Whereas, based on PCA plots and Circos plot, the microbial community structure has changed significantly. LEfSe method was used to identify the classified bacterial taxa with significant abundance differences between the low water level and high water level periods. KOs (KEGG Orthology) pathway enrichment analysis were conducted to investigate functional and related metabolic pathways in groups. To some extent, it can be inferred that water level regulation affects community growth by affecting the metabolism of the microbial community. [ABSTRACT FROM AUTHOR]

Anthropogenic activities and increased land use, which include industrialization, agriculture and urbanization, directly affect pollinators by changing habitats and floral availability, and indirectly by influencing their microbial composition and diversity. Bees form vital symbioses with their microbiota, relying on microorganisms to perform physiological functions and aid in immunity. As altered environments and climate threaten bees and their microbiota, characterizing the microbiome and its complex relationships with its host offers insights into understanding bee health. This review summarizes the role of sociality in microbiota establishment, as well as examines if such factors result in increased susceptibility to altered microbiota due to environmental changes. We characterize the role of geographic distribution, temperature, precipitation, floral resources, agriculture, and urbanization on bee microbiota. Bee microbiota are affected by altered surroundings regardless of sociality. Solitary bees that predominantly acquire their microbiota through the environment are particularly sensitive to such effects. However, the microbiota of obligately eusocial bees are also impacted by environmental changes despite typically well conserved and socially inherited microbiota. We provide an overview of the role of microbiota in plant-pollinator relationships and how bee microbiota play a larger role in urban ecology, offering microbial connections between animals, humans, and the environment. Understanding bee microbiota presents opportunities for sustainable land use restoration and aiding in wildlife conservation. [ABSTRACT FROM AUTHOR]

Microbial life in low‐energy ecosystems relies on individual energy conservation, optimizing energy use in response to interspecific competition and mutualistic interspecific syntrophy. Our study proposes a novel community‐level strategy for increasing energy use efficiency. By utilizing an oxidation–reduction (redox) reaction network model that represents microbial redox metabolic interactions, we investigated multiple species‐level competition and cooperation within the network. Our results suggest that microbial functional diversity allows for metabolic handoffs, which in turn leads to increased energy use efficiency. Furthermore, the mutualistic division of labour and the resulting complexity of redox pathways actively drive material cycling, further promoting energy exploitation. Our findings reveal the potential of self‐organized ecological interactions to develop efficient energy utilization strategies, with important implications for microbial ecosystem functioning and the co‐evolution of life and Earth. [ABSTRACT FROM AUTHOR]

The aim of this study was to investigate the microbial diversity encompassing bacteria, fungi, and viruses within the composite microbial community associated with Aedes aegypti mosquitoes in Manado, Indonesia, using a whole-genome shotgun metagenomics approach. Female mosquitoes were collected and grouped into pools of 50 individuals, from which genomic DNA (gDNA) and RNA were extracted separately. Whole-genome shotgun metagenomics were performed on gDNA samples. The bioinformatics analysis encompassed quality assessment, taxonomic classification, and visualization. The evaluation of the microbial community entailed an assessment of taxa abundance and diversity using Kraken version 2.1.2. The study delineated the prevalence of dominant bacterial phyla, including Proteobacteria, with varying abundance of Firmicutes, Bacteroidota, and Actinobacteria, and notable occurrence of Tenericutes. Furthermore, the presence of the fungal phylum Ascomycota was also detected. Among the identified barcodes, Barcode04 emerged as the most abundant and diverse, while Barcode06 exhibited greater evenness. Barcode03, 05, and 07 displayed moderate richness and diversity. Through an analysis of the relative abundance, a spectrum of viruses within Ae. aegypti populations was unveiled, with Negarnaviricota constituting the most prevalent phylum, followed by Nucleocytoviricota, Uroviricota, Artverviricota, Kitrinoviricota, Peploviricota, Phixviricota, and Cossaviricota. The presence of Negarnaviricota viruses raises pertinent public health concerns. The presence of other viral phyla underscores the intricate nature of virus–mosquito interactions. The analysis of viral diversity provides valuable insights into the range of viruses carried by Ae. aegypti. The community exhibits low biodiversity, with a few dominant species significantly influencing its composition. This has implications for healthcare and ecological management, potentially simplifying control measures but also posing risks if the dominant species are harmful. This study enriches our comprehension of the microbiome and virome associated with Ae. aegypti mosquitoes, emphasizing the importance of further research to fully comprehend their ecological significance and impact on public health. The findings shed light on the microbial ecology of Ae. aegypti, offering potential insights into mosquito biology, disease transmission, and strategies for vector control. Future studies should endeavor to establish specific associations with Ae. aegypti, elucidate the functional roles of the identified microbial and viral species, and investigate their ecological implications. [ABSTRACT FROM AUTHOR]

Clostridioides difficile colonizes a polymicrobial environment in the intestine and is a causative agent for antibioticassociated diarrhea (AAD) and pseudomembranous colitis (PMC). The most important virulence factors of C. difficile are bacterial toxins, and three toxins (toxin A, toxin B, and binary toxin) are produced by toxigenic strains. Other virulence factors include spores, flagella, capsules, biofilms, hydrolytic enzymes and adhesins. C. difficile infection (CDI) is specifically diagnosed by anaerobic culture and toxin detection by either nucleic acid amplification test (NAAT) or enzyme-linked immunosorbent assay (ELISA). For treatment of CDI, metronidazole, vancomycin and fidaxomicin are used based on the severity of CDI. Mutual interaction between C. difficile and gut microbiota is associated with pathogenesis of CDI, and decreased microbial diversity with altered gut microbiome was detected in CDI patients. Restoration of certain gut microbiota is considered to be potentially effective for the prevention and treatment of CDI, and an ideal goal for CDI patients is restoration of the gut microbiota to a healthy state. Fecal microbiota transplantation (FMT) is a highly successful method of microbiome restoration and has been reported to be effective for the prevention of recurrent CDI. In addition, approaches to restoring the gut microbiota by using probioitcs and live biotherapeutic products (LBPs) are currently being studied to examine the effect on CDI. Further microbial ecological research on C. difficile and gut microbiota could lead to a better understanding of the pathogenesis and treatment of CDI. [ABSTRACT FROM AUTHOR]

The fungal pathogen Zymoseptoria tritici is the causal agent of Septoria tritici blotch (STB), a major wheat disease in Western Europe. Microorganisms inhabiting wheat leaves might act as beneficial, biocontrol, or facilitating agents that could limit or stimulate the development of Z. tritici. Improving our understanding of microbial communities in the wheat phyllosphere would lead to new insights into STB management. This article provides fungal and bacterial metabarcoding datasets obtained by sampling wheat leaves with and without symptoms caused by Z. tritici. Tissues were sampled from three commercial wheat varieties on three sampling dates during a cropping season. Weeds around wheat fields were sampled as well. In total, more than 450 leaf samples were collected. The pathogen Z. tritici was quantified using quantitative PCR. We provide the raw metabarcoding datasets, the amplicon sequence variant tables obtained after bioinformatic processing, the metadata associated with each sample (sampling date, wheat variety and tissue health condition), a preliminary descriptive analysis of the data, and the code used for bioinformatic and descriptive statistical analysis. [Graphic: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Salt marshes are dynamic, highly productive ecosystems positioned at the interface between terrestrial and marine systems. They are exposed to large quantities of both natural and anthropogenic carbon input, and their diverse sediment-hosted microbial communities play key roles in carbon cycling and remineralization. To better understand the effects of natural and anthropogenic carbon on sediment microbial ecology, several sediment cores were collected from Little Sippewissett Salt Marsh (LSSM) on Cape Cod, MA, USA and incubated with either Spartina alterniflora cordgrass or diesel fuel. Resulting shifts in microbial diversity and activity were assessed via bioorthogonal non-canonical amino acid tagging (BONCAT) combined with fluorescence-activated cell sorting (FACS) and 16S rRNA gene amplicon sequencing. Both Spartina and diesel amendments resulted in initial decreases of microbial diversity as well as clear, community-wide shifts in metabolic activity. Multi-stage degradative frameworks shaped by fermentation were inferred based on anabolically active lineages. In particular, the metabolically versatile Marinifilaceae were prominent under both treatments, as were the sulfate-reducing Desulfovibrionaceae, which may be attributable to their ability to utilize diverse forms of carbon under nutrient limited conditions. By identifying lineages most directly involved in the early stages of carbon processing, we offer potential targets for indicator species to assess ecosystem health and highlight key players for selective promotion of bioremediation or carbon sequestration pathways. [ABSTRACT FROM AUTHOR]

The use of museum specimens for research in microbial evolutionary ecology remains an under-utilized investigative dimension with important potential. Despite this potential, there remain barriers in methodology and analysis to the wide-spread adoption of museum specimens for such studies. Here, we hypothesized that there would be significant differences in taxonomic prediction and related diversity among sample type (museum or fresh) and sequencing strategy (medium-depth shotgun metagenomic or 16S rRNA gene). We found dramatically higher predicted diversity from shotgun metagenomics when compared to 16S rRNA gene sequencing in museum and fresh samples, with this differential being larger in museum specimens. Broadly confirming these hypotheses, the highest diversity found in fresh samples was with shotgun sequencing using the Rep200 reference inclusive of viruses and microeukaryotes, followed by the WoL reference database. In museum-specimens, community diversity metrics also differed significantly between sequencing strategies, with the alpha-diversity ACE differential being significantly greater than the same comparisons made for fresh specimens. Beta diversity results were more variable, with significance dependent on reference databases used. Taken together, these findings demonstrate important differences in diversity results and prompt important considerations for future experiments and downstream analyses aiming to incorporate microbiome datasets from museum specimens. [ABSTRACT FROM AUTHOR]

Environmental heterogeneity is an important factor in affecting microbial community structure and diversity, which contains a variety of interrelated elements. Based on the biotic and abiotic characteristics, environmental heterogeneity can be divided into five categories, land cover, vegetation, climate, soil, and topography. This paper summarized the concepts and differences of the above five types of environmental heterogeneity, and the effects of which on microbial community were comprehensively collected and analyzed. Through combing the development of microbial ecology, bioinformatics and other relevant research methods, the shortages of the current research on the interactions between environmental heterogeneity and microorganisms were outlined, and the future research trends were prospected. [ABSTRACT FROM AUTHOR]