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Benthic cyanobacterial mats are increasing in abundance worldwide with the potential to degrade ecosystem structure and function. Understanding mat community dynamics is thus critical for predicting mat growth and proliferation and for mitigating any associated negative effects. Carbon, nitrogen, and sulfur cycling are the predominant forms of nutrient cycling discussed within the literature, while metabolic cooperation and viral interactions are understudied. Although many forms of nutrient cycling in mats have been assessed, the links between niche dynamics, microbial interactions, and nutrient cycling are not well described. Here, we present an updated review on how nutrient cycling and microbial community interactions in mats are structured by resource partitioning via spatial and temporal heterogeneity and succession. We assess community interactions and nutrient cycling at both intramat and metacommunity scales. Additionally, we present ideas and recommendations for research in this area, highlighting top-down control, boundary layers, and metabolic cooperation as important future directions., (© 2024 Phycological Society of America.)

Marine sponges host diverse microbial communities. Although we know many of its ecological patterns, a deeper understanding of the polar sponge holobiont is still needed. We combine high-throughput sequencing of ribosomal genes, including the largest taxonomic repertoire of Antarctic sponge species analyzed to date, functional metagenomics, and metagenome-assembled genomes (MAGs). Our findings show that sponges harbor more exclusive bacterial and archaeal communities than seawater, while microbial eukaryotes are mostly shared. Furthermore, bacteria in Antarctic sponge holobionts establish more cooperative interactions than in sponge holobionts from other environments. The bacterial classes that established more positive relations were Bacteroidia, Gamma- and Alphaproteobacteria. Antarctic sponge microbiomes contain microbial guilds that encompass ammonia-oxidizing archaea, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, and sulfur-oxidizing bacteria. The retrieved MAGs showed a high level of novelty and streamlining signals and belong to the most abundant members of the main microbial guilds in the Antarctic sponge holobiont. Moreover, the genomes of these symbiotic bacteria contain highly abundant functions related to their adaptation to the cold environment, vitamin production, and symbiotic lifestyle, helping the holobiont survive in this extreme environment., (© 2024. The Author(s).)

The microbiota within the guts of insects plays beneficial roles for their hosts, such as facilitating digestion and extracting energy from their diet. The African palm weevil (APW) lives within and feeds on the high lignin-containing trunk of palm trees; therefore, their guts could harbour a large community of lignin-degrading microbes. In this study, we aimed to explore the bacterial community within the gut of the APW larvae, specifically with respect to the potential for lignin degradation in various gut segments as a first step to determining the viability of mining bacterial lignin-degrading enzymes for the bioconversion of lignocellulosic biomass to biofuels and biomaterials. Bacterial metagenomic DNA was extracted from the foregut, midgut, and hindgut of larvae of the APW, and the V3–V4 hypervariable region of the 16S rRNA gene was sequenced using the Illumina MiSeq platform. The generated data were analysed and taxonomically classified to identify the different bacterial phylotypes within the gut community cumulatively and per gut segment. We then determined the presence, diversity, and abundance of bacteria associated with lignin degradation within each larval gut compartment as a basis for suggesting the gut segment(s) where lignin degradation occurs the most. All sequences were classified and belonged to the bacterial kingdom. Firmicutes (54.3%) and Proteobacteria (42.5%) were the most dominant phyla within the gut, followed distantly by Bacteroidota (1.7%) and Actinobacteriota (1.4%). Enterococcus , Levilactobacillus , Lactococcus , Shimwellia , Megasphaera , Klebsiella , Pectinatus , Salmonella , Lelliotia , and Enterobacter constituted the most abundant genera found across all gut segments. The foregut and midgut had many similar genera, whilst the hindgut appeared unique. Overall, 29.5% of total gut bacteria comprising 21 genera were lignin degraders found predominantly in the Firmicutes and Proteobacteria phyla (56.8 and 39.5%, respectively), then moderately in Actinobacteriota (2.5%) and Bacteroidota (1.1%). The most abundant ligninolytic genera were Levilactobacillus (46.4%), Klebsiella (22.9%), Enterobacter (10.7%), Lactiplantibacillus (5.9%), Citrobacter (2.2%), Corynebacterium (1.8%), Paucilactobacillus (1.8%), Serratia (1.5%), Bacteroides (1.1%), and Leucobacter (1.0%) found in different amounts in different gut compartments. The foregut had the most diverse and highest abundance of lignin-degrading phylotypes, and we present reasons that point to the foregut as the main location for the depolymerization of lignin in the APW larval gut. [ABSTRACT FROM AUTHOR]

Diplocarpon coronariae is a fungal pathogen that is prevalent in low-input apple production. Over the past 15 years, it has become increasingly distributed in Europe. However, comprehensive insights into its biology and pathogenicity remain limited. One particular aspect is the rarity of the sexual morph of this pathogen, a phenomenon hitherto unobserved in Europe. Diplocarpon coronariae reproduces through a heterothallic mating system requiring at least two different mating types for sexual reproduction. Genes determining the mating types are located on the mating-type locus. In this study, D. coronariae strain DC1_JKI from Dresden, Germany, was sequenced and used to unravel the structure of the mating type locus. Using short-read and long-read sequencing methods, the first gapless and near-complete telomere-to-telomere genome assembly of D. coronariae was achieved. The assembled genome spans 51.2 Mbp and comprises 21 chromosome-scale contigs of high completeness. The generated genome sequence was used to in silico elucidate the structure of the mating-type locus, identified as MAT1-2. Furthermore, an examination of MAT1-1 and MAT1-2 frequency across a diverse set of samples sourced from Europe and Asia revealed the exclusive presence of MAT1-2 in European samples, whereas both MAT loci were present in Asian counterparts. Our findings suggest an explanation for the absence of the sexual morph, potentially linked to the absence of the second mating idiomorph of D. coronariae in European apple orchards. [ABSTRACT FROM AUTHOR]

Introduction: The demand for gluconic acid (GA) has risen recently, driven by its extensive applications in the food, healthcare, and construction industries. The biocatalysis of gluconic acid, facilitated by glucose oxidase and catalase, hinges on enzyme stability, significantly influencing catalytic efficiency. Nonetheless, catalase requires enhancements in thermal stability and activity to meet the requirements of practical applications. Methods: We evaluated ten catalases expressed in Aspergillus niger , ultimately selecting the catalase from the thermophilic fungus Thermoascus aurantiacus , labeled as TaCat, for its superior thermal stability and operational performance. We further characterized the enzymatic properties of the recombinant catalase, focusing on its thermostability. Simultaneously, we used AlphaFold2 for structural predictions and conducted in-depth analyses via accelerated molecular dynamics simulations. Results and discussion: We successfully obtained a strain with the highest catalase activity by optimizing signal peptides and overexpressing the crucial heme synthesis enzyme. Enzyme production reached an impressive 321,779.5 U/mL in a 50-L fermenter. Our application studies confirmed the considerable advantages of TaCat in terms of GA production. In conclusion, TaCat, distinguished by its remarkable thermal stability and high activity, holds substantial potential for GA production. [ABSTRACT FROM AUTHOR]

Large-scale land reclamation has become common in northwestern China; however, low soil fertility and poor soil water-holding capacity limit agricultural production on these reclaimed lands, requiring increased fertilizer and irrigation inputs. Biochar, produced from agricultural waste, has shown potential in improving soil quality and water-holding capacity. In this two-year field study (2021 and 2022), we investigated the effects of biochar produced from maize straw on soil properties and grain yield of foxtail millet grown on newly reclaimed land. Three biochar treatments (3000, 4500, and 6000 kg ha−1) were compared to a control (CK) with no biochar application. Biochar application resulted in increased soil organic matter, total phosphorus, total nitrogen, soil enzyme activity, and soil organic acid content. It also significantly decreased soil pH and bulk density. Compared with the CK, biochar increased available nitrogen from 29.7% to 108% in 2021 and 37.0% to 88.4% in 2022. Similarly, biochar increased available phosphorus from 64.7% to 143% in 2021 and 41.9% to 96.5% in 2022. Grain yields ranged from 3092 to 4753 kg ha−1. Biochar treatments increased grain yield compared to the CK, ranging from 12.2% to 24.6% in 2021 and 27.1% to 53.7% in 2022. Correlation analysis revealed that soil pH was negatively related to soil oxalic acid content, phosphorus content, and sucrase activity. Available nitrogen and phosphorus contents were negatively related to soil bulk density and positively related to catalase activity. Soil water content was negatively correlated with soil bulk density and positively correlated with organic matter. In conclusion, biochar improved the rhizosphere soil pH and the effectiveness of soil fertility in the newly reclaimed soil, resulting in an enhanced grain yield of foxtail millet. [ABSTRACT FROM AUTHOR]

The increasing reliance on fossil fuels and the growing accumulation of organic waste necessitates the exploration of sustainable energy alternatives. Anaerobic digestion (AD) presents one such solution by utilizing secondary biomass to produce biogas while reducing greenhouse gas emissions. Given the crucial role of microbial activity in anaerobic digestion, a deeper understanding of the microbial community is essential for optimizing biogas production. While metagenomics has emerged as a valuable tool for unravelling microbial composition and providing insights into the functional potential in biodigestion, it falls short of interpreting the functional and metabolic interactions, limiting a comprehensive understanding of individual roles in the community. This emphasizes the significance of expanding the scope of metagenomics through innovative tools that highlight the often-overlooked, yet crucial, role of microbiota in biomass digestion. These tools can more accurately elucidate microbial ecological fitness, shared metabolic pathways, and interspecies interactions. By addressing current limitations and integrating metagenomics with other omics approaches, more accurate predictive techniques can be developed, facilitating informed decision-making to optimize AD processes and enhance biogas yields, thereby contributing to a more sustainable future. [ABSTRACT FROM AUTHOR]

The average American spends 93% of their time in built environments, almost 70% of that is in their place of residence. Human health and well-being are intrinsically tied to the quality of our personal environments and the microbiomes that populate them. Conversely, the built environment microbiome is seeded, formed, and re-shaped by occupant behavior, cleaning, personal hygiene and food choices, as well as geographic location and variability in infrastructure. Here, we focus on the presence of viruses in household biofilms, specifically in showerheads and on toothbrushes. Bacteriophage, viruses that infect bacteria with high host specificity, have been shown to drive microbial community structure and function through host infection and horizontal gene transfer in environmental systems. Due to the dynamic environment, with extreme temperature changes, periods of wetting/drying and exposure to hygiene/cleaning products, in addition to low biomass and transient nature of indoor microbiomes, we hypothesize that phage host infection in these unique built environments are different from environmental biofilm interactions. We approach the hypothesis using metagenomics, querying 34 toothbrush and 92 showerhead metagenomes. Representative of biofilms in the built environment, these interfaces demonstrate distinct levels of occupant interaction. We identified 22 complete, 232 high quality, and 362 medium quality viral OTUs. Viral community richness correlated with bacterial richness but not Shannon or Simpson indices. Of quality viral OTUs with sufficient coverage (614), 532 were connected with 32 bacterial families, of which only Sphingomonadaceae, Burkholderiaceae, and Caulobacteraceae are found in both toothbrushes and showerheads. Low average nucleotide identity to reference sequences and a high proportion of open reading frames annotated as hypothetical or unknown indicate that these environments harbor many novel and uncharacterized phage. The results of this study reveal the paucity of information available on bacteriophage in indoor environments and indicate a need for more virusfocused methods for DNA extraction and specific sequencing aimed at understanding viral impact on the microbiome in the built environment. [ABSTRACT FROM AUTHOR]

The production of lignocellulytic enzymes by microwave-radiated Pleurotus sajor-caju was assayed. Wheat straw was employed as substrate to P. sajor-caju for production of laccase, manganese peroxidase (MnPase), filter-paperase (FPase), carboxmethyl cellulase (CMCase), and cellulase (as evaluated using microcrystalline cellulose). P. sajor-caju exposed to 10 s of microwave radiation (MR) showed maximum growth with colony radius of 7.17 ± 0.45 cm, while with increasing the exposure time up to 50 s the growth decreased up to 2.67 ± 0.22 cm. Moreover, it failed to grow at 80 s of exposure time. Cellulase, MnPase, FPase, CMCase, and laccase activities were induced to 37 ± .0.54, 49 ± 2.36, 189 ± 2.12, 0.37 ± 0.06, and 1.58 ± 0.03 U/mL compared to that at control 31 ± 0.25, 46 ± 1.25, 177 ± 1.65, 0.28 ± 0.03, and 1.37 ± 0.12 U/mL, respectively as a result of P. sajor-caju exposure to 10 s of MR. As the exposure time increased, these enzymes activity decreased. Different levels of moisture with surfactant (polysorbate 80) were applied to optimize the enzymes activities at 10 s of exposure time. The optimum activities 3.15 ± 0.23, 0.62 ± 0.06, 269 ± 5.36, 65 ± 1.63, and 48 ± 0.98 U/mL were recorded for cellulase, MnPase, FPase, CMCase, and laccase, respectively at 70% of moisture and 0.15 mL/L of polysorbate 80. [ABSTRACT FROM AUTHOR]

Hydrothermal vents host a diverse community of microorganisms that utilize chemical gradients from the venting fluid for their metabolisms. The venting fluid can solidify to form chimney structures that these microbes adhere to and colonize. These chimney structures are found throughout many different locations in the world's oceans. In this study, comparative metagenomic analyses of microbial communities on five chimney structures from around the Pacific Ocean were elucidated focusing on the core taxa and genes that are characteristic of each of these hydrothermal vent chimneys. The differences among the taxa and genes found at each chimney due to parameters such as physical characteristics, chemistry, and activity of the vents were highlighted. DNA from the chimneys was sequenced, assembled into contigs, and annotated for gene function. Genes used for carbon, oxygen, sulfur, nitrogen, iron, and arsenic metabolisms were found at varying abundances at each of the chimneys, largely from either Gammaproteobacteria or Campylobacteria. Many taxa shared an overlap of these functional metabolic genes, indicating that functional redundancy is critical for life at these hydrothermal vents. A high relative abundance of oxygen metabolism genes coupled with a low abundance of carbon fixation genes could be used as a unique identifier for inactive chimneys. Genes used for DNA repair, chemotaxis, and transposases were found at high abundances at each of these hydrothermal chimneys allowing for enhanced adaptations to the ever-changing chemical and physical conditions encountered. [ABSTRACT FROM AUTHOR]

Here we present the construction and characterization of metagenome assembled genomes (MAGs) from two hot springs residing in the vicinity of Indian Himalayan Geothermal Belt (IHGB). A total of 78 and 7 taxonomic bins were obtained for Old Yume Samdong (OYS) and New Yume Samdong (NYS) hot springs respectively. After passing all the criteria only 21 and 4 MAGs were further studied based on the successful prediction of their 16 S rRNA. Various databases were used such as GTDB, Kaiju, EzTaxon, BLAST XY Plot and NCBI BLAST to get the taxonomic classification of various 16 S rRNA predicted MAGs. The bacterial genomes found were from both thermophilic and mesophilic bacteria among which Proteobacteria, Chloroflexi, Bacteroidetes and Firmicutes were the abundant phyla. However, in case of OYS, two genomes belonged to archaeal Methanobacterium and Methanocaldococcus. Functional characterization revealed the richness of CAZymes such as Glycosyl Transferase (GT) (56.7%), Glycoside Hydrolase (GH) (37.4%), Carbohydrate Esterase family (CE) (8.2%), and Polysaccharide Lyase (PL) (1.9%). There were negligible antibiotic resistance genes in the MAGs however, a significant heavy metal tolerance gene was found in the MAGs. Thus, it may be assumed that there is no coexistence of antibiotic and heavy metal resistance genes in these hot spring microbiomes. Since the selected hot springs possess good sulfur content thus, we also checked the presence of genes for sulfur and nitrogen metabolism. It was found that MAGs from both the hot springs possess significant number of genes related to sulfur and nitrogen metabolism., (© 2023. The Author(s), under exclusive licence to Springer Nature B.V.)

Candidate bacterial phylum Omnitrophota has not been isolated and is poorly understood. We analysed 72 newly sequenced and 349 existing Omnitrophota genomes representing 6 classes and 276 species, along with Earth Microbiome Project data to evaluate habitat, metabolic traits and lifestyles. We applied fluorescence-activated cell sorting and differential size filtration, and showed that most Omnitrophota are ultra-small (~0.2 μm) cells that are found in water, sediments and soils. Omnitrophota genomes in 6 classes are reduced, but maintain major biosynthetic and energy conservation pathways, including acetogenesis (with or without the Wood-Ljungdahl pathway) and diverse respirations. At least 64% of Omnitrophota genomes encode gene clusters typical of bacterial symbionts, suggesting host-associated lifestyles. We repurposed quantitative stable-isotope probing data from soils dominated by andesite, basalt or granite weathering and identified 3 families with high isotope uptake consistent with obligate bacterial predators. We propose that most Omnitrophota inhabit various ecosystems as predators or parasites., (© 2023. The Author(s).)

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Porphyra haitanensis (P. haitanensis), an important food source for coastal residents in China, has a long history of medicinal and edible value. P. haitanensis polysaccharides are some of the main active ingredients in P. haitanensis. It is worth noting that P. haitanensis polysaccharides have a surprising and satisfactory biological activity, which explains the various benefits of P. haitanensis to human health, such as anti-oxidation, immune regulation, anti-allergy, and anticancer properties. Hence, a systematic review aimed at comprehensively summarizing the recent research advances in P. haitanensis polysaccharides is necessary for promoting their better understanding. In this review, we systematically and comprehensively summarize the research progress on the extraction, purification, structural characterization, modification, and biological activity of P. haitanensis polysaccharides and address the shortcomings of the published research and suggest area of focus for future research, providing a new reference for the exploitation of polysaccharides from P. haitanensis in the fields of medicine and functional foods. [ABSTRACT FROM AUTHOR]

Microbial inhibition by high ammonia concentrations is a recurring problem that significantly restricts methane formation from intermediate acids, i.e., propionate and acetate, during anaerobic digestion of protein-rich waste material. Studying the syntrophic communities that perform acid conversion is challenging, due to their relatively low abundance within the microbial communities typically found in biogas processes and disruption of their cooperative behavior in pure cultures. To overcome these limitations, this study examined growth parameters and microbial community dynamics of highly enriched mesophilic and ammonia-tolerant syntrophic propionate and acetate-oxidizing communities and analyzed their metabolic activity and cooperative behavior using metagenomic and metatranscriptomic approaches. Cultivation in batch set-up demonstrated biphasic utilization of propionate, wherein acetate accumulated and underwent oxidation before complete degradation of propionate. Three key species for syntrophic acid degradation were inferred from genomic sequence information and gene expression: a syntrophic propionate-oxidizing bacterium (SPOB) “Candidatus Syntrophopropionicum ammoniitolerans”, a syntrophic acetate-oxidizing bacterium (SAOB) Syntrophaceticus schinkii and a novel hydrogenotrophic methanogen, for which we propose the provisional name “Candidatus Methanoculleus ammoniitolerans”. The results revealed consistent transcriptional profiles of the SAOB and the methanogen both during propionate and acetate oxidation, regardless of the presence of an active propionate oxidizer. Gene expression indicated versatile capabilities of the two syntrophic bacteria, utilizing both molecular hydrogen and formate as an outlet for reducing equivalents formed during acid oxidation, while conserving energy through build-up of sodium/proton motive force. The methanogen used hydrogen and formate as electron sources. Furthermore, results of the present study provided a framework for future research into ammonia tolerance, mobility, aggregate formation and interspecies cooperation. [ABSTRACT FROM AUTHOR]

Hydrocarbon pollution is a widespread issue in both groundwater and surfacewater systems; however, research on remediation at the interface of these two systems is limited. This interface is the oxic-anoxic boundary, where hydrocarbon pollutant from contaminated groundwaters flows into surface waters and iron mats are formed by microaerophilic iron-oxidizing bacteria. Iron mats are highly chemically adsorptive and host a diverse community of microbes. To elucidate the effect of hydrocarbon exposure on iron mat geochemistry and microbial community structure and function, we sampled iron mats both upstream and downstream from a leaking underground storage tank. Hydrocarbon-exposed iron mats had significantly higher concentrations of oxidized iron and significantly lower dissolved organic carbon and total dissolved phosphate than unexposed iron mats. A strong negative correlation between dissolved phosphate and benzene was observed in the hydrocarbonexposed iron mats and water samples. There were positive correlations between iron and other hydrocarbons with benzene in the hydrocarbon-exposed iron mats, which was unique from water samples. The hydrocarbon-exposed iron mats represented two types, flocculent and seep, which had significantly different concentrations of iron, hydrocarbons, and phosphate, indicating that iron mat is also an important context in studies of freshwater mats. Using constrained ordination, we found the best predictors for community structure to be dissolved oxygen, pH, and benzene. Alpha diversity and evenness were significantly lower in hydrocarbon-exposed iron mats than unexposed mats. Using 16S rDNA amplicon sequences, we found evidence of three putative nitrate-reducing iron-oxidizing taxa in microaerophile-dominated iron mats (Azospira, Paracoccus, and Thermomonas). 16S rDNA amplicons also indicated the presence of taxa that are associated with hydrocarbon degradation. Benzene remediation-associated genes were found using metagenomic analysis both in exposed and unexposed iron mats. Furthermore, the results indicated that season (summer vs. spring) exacerbates the negative effect of hydrocarbon exposure on community diversity and evenness and led to the increased abundance of numerous OTUs. This study represents the first of its kind to attempt to understand how contaminant exposure, specifically hydrocarbons, influences the geochemistry and microbial community of freshwater iron mats and further develops our understanding of hydrocarbon remediation at the land-water interface. [ABSTRACT FROM AUTHOR]

Changes in climatic factors and rhizosphere microbiota led plants to adjust their metabolic strategies for survival under adverse environmental conditions. Changes in plant metabolites can mediate crop growth and development and interact with rhizosphere microbiota of the plant rhizosphere. To understand the interactions among environmental factors, rhizosphere microbiota, and metabolites of tobacco, a study was conducted by using integrated metagenomic and metabolomic strategies at four typical representative tobacco planting sites in Yunnan, China. The results showed that the agronomical and biochemical traits were significantly affected by temperature, precipitation (PREP), soil pH, and altitude. Correlation analyses revealed a significant positive correlation of temperature with length, width, and area of the leaf, while PREP correlated with plant height and effective leaf numbers. Furthermore, total sugar and reducing sugar contents of baked leaves were significantly higher, while the total nitrogen and total alkaloid levels were lower in tobacco leaves at site with low PREP. A total of 770 metabolites were detected with the highest number of different abundant metabolites (DMs) at Chuxiong (CX) with low PREP as compared to the other three sites, in which secondary metabolites were more abundant in both leaves and roots of tobacco. A total of 8,479 species, belonging to 2,094 genera with 420 individual bins (including 13 higher-quality bins) harboring 851,209 CDSs were detected. The phyla levels of microorganisms such as Euryarchaeota, Myxococcota, and Deinococcota were significantly enriched at the CX site, while Pseudomonadota was enriched at the hightemperature site with good PREP. The correlation analyses showed that the metabolic compounds in low-PREP site samples were positively correlated with Diaminobutyricimonas, Nissabacter, Alloactinosynnema, and Catellatospora and negatively correlated with Amniculibacterium, Nordella, Noviherbaspirillum, and Limnobacter, suggesting that the recruitment of Diaminobutyricimonas, Nissabacter, Alloactinosynnema, and Catellatospora in the rhizosphere induces the production and accumulation of secondary metabolites (SMs) (e.g., nitrogen compounds, terpenoids, and phenolics) for increasing drought tolerance with an unknown mechanism. The results of this study may promote the production and application of microbial fertilizers and agents such as Diaminobutyricimonas and Alloactinosynnema to assemble synthetic microbiota community or using their gene resources for better cultivation of tobacco as well as other crops in drought environments. [ABSTRACT FROM AUTHOR]

Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only become possible recently. To realize the hope of capturing Earth's microbial genetic complement and to facilitate the investigation of the functional roles of specific lineages in a given ecosystem, technologies that accelerate the recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high-quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform ( http://www.kbase.us/ ). Overall, these steps take about a day to obtain extracted genomes when starting from smaller environmental shotgun read libraries, or up to about a week from larger libraries. In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAGs, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq and others. While portions of such capabilities are available individually from other resources, the combination of the intuitive usability, data interoperability and integration of tools in a freely available computational resource makes KBase a powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended with additional MAG recovery and analysis tools, via the KBase software development kit (SDK)., (© 2022. Springer Nature Limited.)

Glacier-fed streams (GFS) feature among Earth's most extreme aquatic ecosystems marked by pronounced oligotrophy and environmental fluctuations. Microorganisms mainly organize in biofilms within them, but how they cope with such conditions is unknown. Here, leveraging 156 metagenomes from the Vanishing Glaciers project obtained from sediment samples in GFS from 9 mountains ranges, we report thousands of metagenome-assembled genomes (MAGs) encompassing prokaryotes, algae, fungi and viruses, that shed light on biotic interactions within glacier-fed stream biofilms. A total of 2,855 bacterial MAGs were characterized by diverse strategies to exploit inorganic and organic energy sources, in part via functional redundancy and mixotrophy. We show that biofilms probably become more complex and switch from chemoautotrophy to heterotrophy as algal biomass increases in GFS owing to glacier shrinkage. Our MAG compendium sheds light on the success of microbial life in GFS and provides a resource for future research on a microbiome potentially impacted by climate change., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Microorganisms change the properties of microplastics, at the same time, microplastics can also affect the distribution of microorganisms. To investigate this issue, we chose to study Jianhu Lake, a plateau lake in southwestern China, by collecting data at three sampling locations. The microplastics and bacterial communities in the sediment columns of Jianhu Lake were sampled within a 0 to 60 cm profile, and the basic characteristics of microplastic abundance, shape, color, size, and polymer type were determined accordingly, via their collection, separation, extraction, and identification. The bacterial community in the sediment samples were identified using 16S rRNA high-throughput sequencing, and we assessed whether those microplastic characteristics influenced the community composition and structure. We found the abundance of microplastics ranged from 624 to 3050 particles/kg (dw [dry weight]) in the three sediment columns. Line microplastics accounted for the largest proportion and these were found distributed in each layer. The polymer types present in the largest proportions were rayon (RY), polyester terephthalate (PET) and low-density styrene-butadiene-styrene (SBS). Among the bacterial communities in the sediment columns, the dominant phyla were Chloroflexi, Sva0485, Acidobacteriota, etc. The co-occurrence network analysis between the bacterial community and microplastic features in the sediment columns of Jianhu Lake revealed that there was a correlation between them, and the network were more complex at a depth of 20-40 cm. Our results demonstrate that microplastics can affect the diversity and structural characteristics of microbial communities in a lake ecosystem., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Cyanobacteria exhibit a vast diversity from polar to tropical environments. Though much work has been done on elucidating their biodiversity, knowledge on the occurrence, diversity and toxicity of benthic cyanobacteria is limited when compared to the planktonic forms. Integrating molecular techniques with ecological and morphological analyses has become essential in untangling cyanobacterial diversity, particularly for benthic taxa such as the cryptic "Lyngbya." Molecular markers such as the 16S rRNA gene and whole genome sequencing have significantly improved the taxonomy of cyanobacteria. Building on these advancements, this study characterizes benthic cyanobacterial isolates from various locations in Florida, USA, and Orange Walk, Belize, resulting in the identification of a novel genus, Floridanema, and four new species (F. aerugineum, F. evergladense, F. flaviceps, and F. fluviatile). This new genus commonly occurs in canals, ponds, lakes and rivers. By integrating ecological, morphological, and genomic analyses, this study provides support for the family Aerosakkonemataceae and the establishment of the order Aerosakkonematales. The LC-MS data revealed that Floridanema strains do not produce microcystins, nodularin-R, or anabaenopeptins., (© 2024 Phycological Society of America.)

Lake Mattamuskeet, the largest lake in North Carolina, USA, has undergone decades-long eutrophication causing reduced water quality and promoting cyanobacterial blooms that may produce toxins. It is therefore necessary to evaluate the cyanobacterial diversity of the lake and their toxigenic potential. We present draft genomes of Microcystis, Pelatocladus, Raphidiopsis, and Umezakia strains isolated from Lake Mattamuskeet. The whole-genome shotgun projects for Umezakia ovalisporum BLCC-F208, Microcystis sp. BLCC-F209, Microcystis sp. BLCC-F210, Pelatocladus sp. BLCC-F211, U. ovalisporum BLCC-F215, and Raphidiopsis BLCC-F218 have been deposited in GenBank under accession numbers JBHFLK000000000, JBHFLL000000000, CP169647, JBHFLM000000000, JBHFLN000000000, and JBHFLO000000000, respectively. Based on the genomic analysis, several biosynthetic gene clusters (BCGs) with varying degrees of similarity to known toxic and bioactive compound gene clusters were identified across the different cyanobacterial strains., (© 2024 Phycological Society of America.)

Microbiomes occupy a range of niches and, in addition to having diverse compositions, they have varied functional roles that have an impact on agriculture, environmental sciences, and human health and disease. The study of microbiomes has been facilitated by recent technological and analytical advances, such as cheaper and higher-throughput DNA and RNA sequencing, improved long-read sequencing and innovative computational analysis methods. These advances are providing a deeper understanding of microbiomes at the genomic, transcriptional and translational level, generating insights into their function and composition at resolutions beyond the species level., Competing Interests: Competing interests The authors declare no competing interests., (© 2024. Springer Nature Limited.)

To ensure sustainable aquaculture, it is essential to understand the path 'from feed to fish', whereby the gut microbiome plays an important role in digestion and metabolism, ultimately influencing host health and growth. Previous work has reported the taxonomic composition of the Atlantic salmon (Salmo salar) gut microbiome; however, functional insights are lacking. Here we present the Salmon Microbial Genome Atlas consisting of 211 high-quality bacterial genomes, recovered by cultivation (n = 131) and gut metagenomics (n = 80) from wild and farmed fish both in freshwater and seawater. Bacterial genomes were taxonomically assigned to 14 different orders, including 35 distinctive genera and 29 previously undescribed species. Using metatranscriptomics, we functionally characterized key bacterial populations, across five phyla, in the salmon gut. This included the ability to degrade diet-derived fibres and release vitamins and other exometabolites with known beneficial effects, which was supported by genome-scale metabolic modelling and in vitro cultivation of selected bacterial species coupled with untargeted metabolomic studies. Together, the Salmon Microbial Genome Atlas provides a genomic and functional resource to enable future studies on salmon nutrition and health., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Heterotrophic activity, primarily driven by sulfate-reducing prokaryotes, has traditionally been linked to nitrogen fixation in the root zone of coastal marine plants, leaving the role of chemolithoautotrophy in this process unexplored. Here, we show that sulfur oxidation coupled to nitrogen fixation is a previously overlooked process providing nitrogen to coastal marine macrophytes. In this study, we recovered 239 metagenome-assembled genomes from a salt marsh dominated by the foundation plant Spartina alterniflora, including diazotrophic sulfate-reducing and sulfur-oxidizing bacteria. Abundant sulfuroxidizing bacteria encode and highly express genes for carbon fixation (RuBisCO), nitrogen fixation (nifHDK) and sulfur oxidation (oxidative-dsrAB), especially in roots stressed by sulfidic and reduced sediment conditions. Stressed roots exhibited the highest rates of nitrogen fixation and expression level of sulfur oxidation and sulfate reduction genes. Close relatives of marine symbionts from the Candidatus Thiodiazotropha genus contributed ~30% and ~20% of all sulfur-oxidizing dsrA and nitrogen-fixing nifK transcripts in stressed roots, respectively. Based on these findings, we propose that the symbiosis between S. alterniflora and sulfur-oxidizing bacteria is key to ecosystem functioning of coastal salt marshes. [ABSTRACT FROM AUTHOR]

Soils exhibit structural heterogeneity across diverse spatio-temporal scales, yielding myriad of microhabitats, highlighting the need for a nuanced understanding of the intricate interactions within the soil matrix. At the nanometer scale, the interplay among organic matter (OM), mineral particles, and microbiota intricately govern the long-term destiny of soil carbon (C), nutrient cycling, and the fate of both organic and inorganic pollutants. Notably, the sorption of soil organic matter (SOM) onto smaller clay particles and its entrapment in microaggregates further contribute to this complex dynamic. Understanding these processes depends on recognizing their scale-dependent nature, necessitating sophisticated techniques for investigation. Although various methods are employed across scales, the current set of techniques still lacks the requisite sensitivity and resolution for microscale data collection. To address this limitation, the adoption of novel microscopic and spectroscopic techniques capable of probing molecular, isotopic, and elemental patterns at the micro to nano scale becomes imperative. Among these cutting-edge methodologies, the nano-scale secondary ion mass spectrometer (NanoSIMS) emerges as a paradigm-shifting tool. Representing the latest evolution in ion microprobes, NanoSIMS seamlessly integrates high-resolution microscopy and isotopic analysis, maintaining unparalleled signal transmission and spatial resolution, reaching as fine as 50 nm. Its capabilities extend beyond conventional applications in science, as evidenced by recent breakthroughs in utilizing NanoSIMS to study biophysical interfaces in soils. This article underscores the pressing need to advance the incorporation of NanoSIMS as a pioneering instrumentation technique in soil studies. Furthering the implementation of this novel instrumentation technique in soil studies will pave avenues and aid in the advancement of future research. [ABSTRACT FROM AUTHOR]

Recent studies have expanded the genomic contours of the Acidithiobacillia, highlighting important lacunae in our comprehension of the phylogenetic space occupied by certain lineages of the class. One such lineage is 'Igneacidithiobacillus', a novel genus-level taxon, represented by 'Igneacidithiobacillus copahuensis' VAN18-1T as its type species, along with two other uncultivated metagenomeassembled genomes (MAGs) originating from geothermally active sites across the Pacific Ring of Fire. In this study, we investigate the genetic and genomic diversity, and the distribution patterns of several uncharacterized Acidithiobacillia class strains and sequence clones, which are ascribed to the same 16S rRNA gene sequence clade. By digging deeper into this data and contributing to novel MAGs emerging from environmental studies in tectonically active locations, the description of this novel genus has been consolidated. Using state-of-the-art genomic taxonomy methods, we added to already recognized taxa, an additional four novel Candidate (Ca.) species, including 'Ca. Igneacidithiobacillus chanchocoensis' (mCHCt20-1TS), 'Igneacidithiobacillus siniensis' (S30A2T), 'Ca. Igneacidithiobacillus taupoensis' (TVZ-G3 TS), and 'Ca. Igneacidithiobacillus waiarikiensis' (TVZ-G4 TS). Analysis of published data on the isolation, enrichment, cultivation, and preliminary microbiological characterization of several of these unassigned or misassigned strains, along with the type species of the genus, plus the recoverable environmental data from metagenomic studies, allowed us to identify habitat preferences of these taxa. Commonalities and lineagespecific adaptations of the seven species of the genus were derived from pangenome analysis and comparative genomic metabolic reconstruction. The findings emerging from this study lay the groundwork for further research on the ecology, evolution, and biotechnological potential of the novel genus 'Igneacidithiobacillus'. [ABSTRACT FROM AUTHOR]

Introduction: Gut microbes form complex networks that significantly influence host health and disease treatment. Interventions with the probiotic bacteria on the gut microbiota have been demonstrated to improve host well-being. As a representative of next-generation probiotics, Christensenella minuta (C. minuta) plays a critical role in regulating energy balance and metabolic homeostasis in human bodies, showing potential in treating metabolic disorders and reducing inflammation. However, interactions of C. minuta with the members of the networked gut microbiota have rarely been explored. Methods: In this study, we investigated the impact of C. minuta on fecal microbiota via metagenomic sequencing, focusing on retrieving bacterial strains and coculture assays of C. minuta with associated microbial partners. Results: Our results showed that C. minuta intervention significantly reduced the diversity of fecal microorganisms, but specifically enhanced some groups of bacteria, such as Lactobacillaceae. C. minuta selectively enriched bacterial pathways that compensated for its metabolic defects on vitamin B1, B12, serine, and glutamate synthesis. Meanwhile, C. minuta cross-feeds Faecalibacterium prausnitzii and other bacteria via the production of arginine, branched-chain amino acids, fumaric acids and short-chain fatty acids (SCFAs), such as acetic. Both metagenomic data analysis and culture experiments revealed that C. minuta negatively correlated with Klebsiella pneumoniae and 14 other bacterial taxa, while positively correlated with F. prausnitzii. Our results advance our comprehension of C. minuta's in modulating the gut microbial network. Conclusions: C. minuta disrupts the composition of the fecal microbiota. This disturbance is manifested through cross-feeding, nutritional competition, and supplementation of its own metabolic deficiencies, resulting in the specific enrichment or inhibition of the growth of certain bacteria. This study will shed light on the application of C. minuta as a probiotic for effective interventions on gut microbiomes and improvement of host health. [ABSTRACT FROM AUTHOR]

This scoping review aims to explore various Deep Learning and Symbolic Artificial Intelligence (AI) models that can be integrated into explainable hybrid AI for the purpose of detecting COVID-19 based on Computerized Tomography (CT) scans. We followed the PRISMA-ScR framework as the foundation for our scoping review protocol. Our approach included a thorough search across 13 databases, complemented by an additional random internet search for relevant articles. Due to the voluminous number of articles returned, the search was further narrowed using the keywords: Deep Learning, Symbolic AI and Hybrid AI. These keywords were used because they are more visible in the earmarked literature. A screening of all articles by title was performed to remove duplicates. The final screening process centered on the publication year, ensuring that all considered articles fell within the range of 2019 to 2023, inclusive. Subsequently, abstract or text synthesis was conducted. Our search query retrieved a total of 3,312 potential articles from the thirteen databases, and an additional 12 articles from a random internet search, resulting in a cumulative count of 3,324 identified articles. After the deduplication and screening steps, 260 articles met our inclusion criteria. These articles were categorized based on the year of publication, the type of aim, and the type of AI used. An analysis of the year of publication revealed a linear trend, indicating growth in the field of Hybrid AI. Out of the five aim categories identified, we deliberately excluded articles that lacked a specified aim. It's noteworthy that 3% of the articles focused on the integration of AI models. The low percentage value suggests that the integration aspect is overlooked, thereby transcripting the integration of Deep Learning and symbolic AI into hybrid AI as an area worth exploring. This scoping review gives an overview of how a Deep Learning and Symbolic AI-based framework has been used in the detection of COVID-19 based on CT scans. [ABSTRACT FROM AUTHOR]

Microbial communities have been used as important biological tools for a variety of purposes associated with agriculture, the food industry and human health. Artificial engineering of microbial communities is an emerging field of research motivated by finding stable and efficient microbial systems. However, the successful design of microbial communities with desirable functions not only requires profound understanding of microbial activities, but also needs efficient approaches to piece together the known microbial traits to give rise to more complex systems. This study demonstrates the bottom-up integration of environmentally isolated phototrophic microalgae and chemotrophic bacteria as artificial consortia to bio-degrade selected volatile organic compounds (VOCs). A high throughput screening method based on 96-well plate format was developed for discovering consortia with bioremediation potential. Screened exemplar consortia were verified for VOCs degradation performance, among these, certain robust consortia were estimated to have achieved efficiencies of 95.72% and 92.70% and near 100% removal (7 days) of benzene, toluene, and phenol, respectively, with initial concentrations of 100 mg/L. VOCs degradation by consortia was mainly attributed to certain bacteria including Rhodococcus erythropolis, and Cupriavidus metallidurans, and directly contributed to the growth of microalgae Coelastrella terrestris (R = 0.82, p < 0.001). This work revealed the potential of converting VOCs waste into algal biomass by algaebacteria consortia constructed through a bottom-up approach. The screening method enables rapid shortlisting of consortia combinatorial scenarios without prior knowledge about the individual strains or the need for interpreting complex microbial interactions. [ABSTRACT FROM AUTHOR]

Poultry enteric bacterial diseases are of significant economic importance because they are responsible for production losses due to weight loss, increased morbidity and mortality, and increased cost of production arising from poor feed conversion and treatment. This cross-sectional purposive study characterized enteric bacterial pathogens in poultry from selected agroclimatic regions in Kenya and investigated their antimicrobial resistance gene profiles. Cloacal (n = 563) and oropharyngeal (n = 394) swabs were collected and pooled into 16 and 14 samples, respectively, to characterize bacterial pathogens and their antimicrobial resistance gene profiles. We report that Proteobacteria, Chlamydiae, and Firmicutes are the most dominant phyla present in both cloacal and oropharyngeal swabs of the six poultry species studied, indicating the colonization of the poultry gut by many pathogenic bacteria. Using KEGG and COG databases, some pathways related to metabolism, genetic information, and cellular processing were detected. We also report the abundance of antimicrobial resistance genes that confer resistance to β-lactamases, aminoglycosides, and tetracycline in most of the poultry analyzed, raising concern about the dangers associated with continuous and inappropriate use of these antibiotics in poultry production. The antimicrobial resistance gene data generated in this study provides a valuable indicator of the use of antimicrobials in poultry in Kenya. The information generated is essential for managing bacterial diseases, especially in backyard poultry raised under scavenging conditions. [ABSTRACT FROM AUTHOR]

Mineral licks are indispensable habitats to the life history of large mammal herbivores (LMH). Geophagy at licks may provide the necessary minerals for LMH, while LMH may be ecosystem engineers of licks by altering vegetation cover and soil physicochemical properties (SPCP). However, the precise relationship between the LMH and licks remains unclear. To clarify the geophagy function of licks for LMH and their influence on soil at licks, we recorded visitation patterns of sika deer around licks and compared SPCP and microbial communities with the surrounding matrix in a firebreak adjacent to the Sino‐Russian border. Our study indirectly supports the "sodium supplementation" hypothesis. Proofs included (1) a significantly higher sodium, iron, and aluminum contents than the matrix, while lower carbon, nitrogen, and moisture contents; (2) significantly higher deer visitation during sodium‐demand season (growing season), along with an avoidance of licks with high iron contents, which is toxic when overdose. The microbes at the licks differed from those at the matrix, mainly driven by low soil carbon and nitrogen and altered biogeochemical cycles. The microbial communities of licks are vulnerable because of their unstable state and susceptibility to SPCP changes. Structural equation modeling (SEM) clearly showed a much stronger indirect effect of deer on microbes at licks than at the matrix, especially for bacteria. Multiple deer behaviors at licks, such as grazing, trampling, and excretion, can indirectly shape and stabilize microbes by altering carbon and nitrogen input. Our study is the first to characterize soil microbial communities at mineral licks and demonstrate the processes by which LMH shapes those communities. More studies are required to establish a general relationship between the LMH and licks to promote the conservation of natural licks for wildlife. [ABSTRACT FROM AUTHOR]

Increasing concerns over environmental pollution, climate change and energy security are driving a necessary transition from fossil carbon sources to more sustainable alternatives. Due to lower environmental impact, biochemicals are rapidly gaining significance as a potential renewable solution, particularly of interest in Europe. In this context, process systems engineering (PSE) helps with the decision-making at multiple scales and levels, aiming for optimum use of (renewable) resources. Fermentation using waste biomass or industrial offgases is a promising way for the production of these products. However, due to the inhibitory effects or low substrate concentrations, relatively low product concentrations can be obtained. Consequently, significant improvements in downstream processing are needed to increase the competitiveness of the overall bioprocesses. This paper supports sustainable development by providing new PSE perspectives on the purification of volatile bioproducts from dilute fermentation broths. Since purification significantly contributes to the total cost of biochemical production processes (20%-40% of the total cost), enhancing this part may substantially improve the competitiveness of the overall bioprocesses. The highly advanced downstream process offers the possibility of recovering high-purity products while enhancing the fermentation step by continuously removing inhibitory products, and recycling microorganisms with most of the present water. Besides higher productivity, the upstream process can be greatly improved by avoiding loss of biomass, enabling closed-loop operation and decreasing the need for fresh water. Applying heat pumping, heat integration and other methods of process intensification (PI) can drastically reduce energy requirements and CO2 emissions. Additionally, the opportunity to use renewable electricity instead of conventional fossil energy presents a significant step toward (green) electrification and decarbonization of the chemical industry. [ABSTRACT FROM AUTHOR]

Microbial syntrophy, a cooperative metabolic interaction among prokaryotes, serves a critical role in shaping communities, due to the auxotrophic nature of many microorganisms. Syntrophy played a key role in the evolution of life, including the hypothesized origin of eukaryotes. In a recent exploration of the microbial mats within the exceptional and uniquely extreme Cuatro Cienegas Basin (CCB), a halophilic isolate, designated as AD140, emerged as a standout due to its distinct growth pattern. Subsequent genome sequencing revealed AD140 to be a co-culture of a halophilic archaeon from the Halorubrum genus and a marine halophilic bacterium, Marinococcus luteus, both occupying the same ecological niche. This intriguing coexistence hints at an early-stage symbiotic relationship that thrives on adaptability. By delving into their metabolic interdependence through genomic analysis, this study aims to uncover shared characteristics that enhance their symbiotic association, offering insights into the evolution of halophilic microorganisms and their remarkable adaptations to high-salinity environments. [ABSTRACT FROM AUTHOR]

Soil organic carbon (SOC) affects the function of terrestrial ecosystem and plays a vital role in global carbon cycle. Yet, large uncertainty still existed regarding the changes in SOC stock and quality with forest succession. Here, the stock and quality of SOC at 1-m soil profile were investigated across a subalpine forest series, including shrub, deciduous broad-leaved forest, broadleaf-conifer mixed forest, middle-age coniferous forest and mature coniferous forest, which located at southeast of Tibetan Plateau. The results showed that SOC stock ranged from 9.8 to 29.9 kg•m-2, and exhibited a hump-shaped response pattern across the forest successional series. The highest and lowest SOC stock was observed in the mixed forest and shrub forest, respectively. The SOC stock had no significant relationships with soil temperature and litter stock, but was positively correlated with wood debris stock. Meanwhile, the average percentages of polysaccharides, lignins, aromatics and aliphatics based on FTIR spectroscopy were 79.89%, 0.94%, 18.87% and 0.29%, respectively. Furthermore, the percentage of polysaccharides exhibited an increasing pattern across the forest successional series except for the sudden decreasing in the mixed forest, while the proportions of lignins, aromatics and aliphatics exhibited a decreasing pattern across the forest successional series except for the sudden increasing in the mixed forest. Consequently, the humification indices (HIs) were highest in the mixed forest compared to the other four successional stages, which means that the SOC quality in mixed forest was worse than other successional stages. In addition, the SOC stock, recalcitrant fractions and HIs decreased with increasing soil depth, while the polysaccharides exhibited an increasing pattern. These findings demonstrate that the mixed forest had higher SOC stock and worse SOC quality than other successional stages. The high proportion of SOC stock (66% at depth of 20-100 cm) and better SOC quality (lower HIs) indicate that deep soil have tremendous potential to store SOC and needs more attention under global change. [ABSTRACT FROM AUTHOR]

The presence of seagrasses facilitates numerous microbial-mediated biogeochemical cycles, with sulfur- and nitrogen-cycling microorganisms playing crucial roles as regulators. Despite efforts to comprehend the diversity of microbes in seagrass ecosystems, the metabolic functions of these benthic microorganisms in seagrass sediments remain largely unknown. Using metagenomics, we provide insights into the sulfur- and nitrogen-cycling pathways and key metabolic capacities of microorganisms in both Z. japonica-colonized and unvegetated sediments over a seasonal period. Taxonomic analysis of N and S cycling genes revealed that δ- and γ- proteobacteria dominated the benthic sulfate-reducing bacteria, while α- and γ-proteobacteria played a significant role in the sulfur-oxidation processes. The proteobacterial lineages were also major contributors to the benthic nitrogen cycling. However, at a finer taxonomic resolution, microbial participants in different processes were observed to be highly diverse and mainly driven by environmental factors such as temperature and salinity. The gene pools of sulfur and nitrogen cycles in the seagrass sediments were dominated by genes involved in sulfide oxidation (fccA) and hydroxylamine oxidation (hao), respectively. Seagrass colonization elevated the relative abundance of genes responsible for sulfite production (phsC), hydroxylamine oxidation (hao), and nitrogen fixation (nifK), but suppressed sulfur oxidation (soxXYZ) and denitrification (nosZ and nirS). The prevalence of proteobacterial lineages functioned with versatile capabilities in both sulfur and nitrogen cycles in seagrass ecosystems, highlighting tight couplings between these processes, which was further supported by the recovery of 83 metagenome-assembled genomes (MAGs). These findings broaden our understanding of the biogeochemical processes that are mediated by microorganisms in seagrass ecosystems. [ABSTRACT FROM AUTHOR]

Stink bug species (Pentatomoidea superfamily) have developed an interdependence with obligate bacterial gut symbionts in specialized midgut crypts (M4 sub-region). Species of the Enterobacteriaceae family (predominantly Pantoea) are vertically transferred to their offspring and provide nutrients that cannot be obtained from plant sap food sources. However, the bacteria in the other gut compartments of stink bugs have rarely been investigated. The two-spotted stink bug, Bathycoelia distincta, is a serious pest of macadamias in South Africa. Nothing is currently known regarding its gut microbiome or how symbionts are transferred between insect generations. In this study, the consistency of B. distincta gut bacteria across geographic locations and life stages was determined with 16S rRNA metabarcoding, considering both the M4 and other gut compartments. A novel Pantoea species was found to be the primary M4 gut symbiont and is vertically transferred to the offspring. The other gut compartments had a low bacterial diversity and genera varied between stink bug populations but a Sodalis species was prominent in all populations. Sequence data of the M4 compartment were used to produce high-quality metagenome-assembled genomes (MAGs) for the Pantoea and Sodalis species. Functional analyses suggested a similar role in nutrient provision for the host, yet also unique metabolites produced by each species. The Sodalis sp. also had additional traits, such as secretion systems, that likely allowed it to establish itself in the host. The Pantoea species was described as Pantoea bathycoeliae sp. nov based on the rules of the SeqCode. [ABSTRACT FROM AUTHOR]

The human microbiome has become an area of intense research due to its potential impact on human health. However, the analysis and interpretation of this data have proven to be challenging due to its complexity and high dimensionality. Machine learning (ML) algorithms can process vast amounts of data to uncover informative patterns and relationships within the data, even with limited prior knowledge. Therefore, there has been a rapid growth in the development of software specifically designed for the analysis and interpretation of microbiome data using ML techniques. These software incorporate a wide range of ML algorithms for clustering, classification, regression, or feature selection, to identify microbial patterns and relationships within the data and generate predictive models. This rapid development with a constant need for new developments and integration of new features require efforts into compile, catalog and classify these tools to create infrastructures and services with easy, transparent, and trustable standards. Here we review the state-of-the-art for ML tools applied in human microbiome studies, performed as part of the COST Action ML4Microbiome activities. This scoping review focuses on ML based software and framework resources currently available for the analysis of microbiome data in humans. The aim is to support microbiologists and biomedical scientists to go deeper into specialized resources that integrate ML techniques and facilitate future benchmarking to create standards for the analysis of microbiome data. The software resources are organized based on the type of analysis they were developed for and the ML techniques they implement. A description of each software with examples of usage is provided including comments about pitfalls and lacks in the usage of software based on ML methods in relation to microbiome data that need to be considered by developers and users. This review represents an extensive compilation to date, offering valuable insights and guidance for researchers interested in leveraging ML approaches for microbiome analysis. [ABSTRACT FROM AUTHOR]

The marine deep subsurface is home to a vast microbial ecosystem, affecting biogeochemical cycles on a global scale. One of the better-studied deep biospheres is the Juan de Fuca (JdF) Ridge, where hydrothermal fluid introduces oxidants into the sediment from below, resulting in two sulfate methane transition zones (SMTZs). In this study, we present the first shotgun metagenomics study of unamplified DNA from sediment samples from different depths in this stratified environment. Bioinformatic analyses showed a shift from a heterotrophic, Chloroflexota-dominated community above the upper SMTZ to a chemolithoautotrophic Proteobacteria-dominated community below the secondary SMTZ. The reintroduction of sulfate likely enables respiration and boosts active cells that oxidize acetate, iron, and complex carbohydrates to degrade dead biomass in this low-abundance, low-diversity environment. In addition, analyses showed many proteins of unknown function as well as novel metagenome-assembled genomes (MAGs). The study provides new insights into microbial communities in this habitat, enabled by an improved DNA extraction protocol that allows a less biased view of taxonomic composition and metabolic activities, as well as uncovering novel taxa. Our approach presents the first successful attempt at unamplified shotgun sequencing samples from beyond 50 meters below the seafloor and opens new ways for capturing the true diversity and functional potential of deep-sea sediments. [ABSTRACT FROM AUTHOR]

Alkanes and alkenes are high-value platform chemicals that can be synthesized by microorganisms, utilizing organic residues from agri-food industries and municipalities, thereby offering an alternative opportunity in resource recovery. Current research and technological advancements for the biosynthesis of alkanes and alkenes are mainly impeded by low product titers, obstructing the bioprocess upscaling and large-scale applications. Thus, current scientific investigations aim to improve productivity by utilizing natural and engineered metabolic pathways in various microbial chassis to suppress competing metabolic pathways, coupled with bioprocess optimization. Additionally, to reduce costs, research is being conducted on utilizing inorganic carbon sources such as CO2 to promote the green synthesis of alkanes and alkenes. Therefore, this review critically discusses the opportunities and challenges in alkane and alkene biosynthesis, aiming to examine the current technological advancements. In this review, the limitations of five major metabolic pathways for alkane and alkene biosynthesis are thoroughly discussed, highlighting their shortcomings. Additionally, various techniques, including metabolic engineering, autotrophic metabolic pathways, and new non-biosynthetic routes, are investigated as potential methods to enhance product titers. Furthermore, this review offers valuable insights into the economic and environmental aspects of alkane and alkene biosynthesis while also presenting perspectives for future research directions. [ABSTRACT FROM AUTHOR]

Adaptive laboratory evolution (ALE) is a technique for the selection of strains with better phenotypes by long-term culture under a specific selection pressure or growth environment. Because ALE does not require detailed knowledge of a variety of complex and interactive metabolic networks, and only needs to simulate natural environmental conditions in the laboratory to design a selection pressure, it has the advantages of broad adaptability, strong practicability, and more convenient transformation of strains. In addition, ALE provides a powerful method for studying the evolutionary forces that change the phenotype, performance, and stability of strains, resulting in more productive industrial strains with beneficial mutations. In recent years, ALE has been widely used in the activation of specific microbial metabolic pathways and phenotypic optimization, the efficient utilization of specific substrates, the optimization of tolerance to toxic substance, and the biosynthesis of target products, which is more conducive to the production of industrial strains with excellent phenotypic characteristics. In this paper, typical examples of ALE applications in the development of industrial strains and the research progress of this technology are reviewed, followed by a discussion of its development prospects. [ABSTRACT FROM AUTHOR]

Benthic cyanobacterial mats (BCMs) are natural phenomena in marine environments. Reports of BCMs occurring across coastal marine environments have increased, partly driven by nutrient loading and climate change; thus, there is a need to understand the diversity involved in the proliferations and potential toxicity of the BCMs. Furthermore, marine cyanobacterial mats are observed growing on and affecting the health of corals with one specific cyanobacterial genus, Roseofilum, dominating the microbial mats associated with black band disease (BBD), a destructive polymicrobial disease that affects corals. To explore the diversity of Roseofilum, cyanobacterial mats from various marine habitats were sampled, and individual isolates were identified based on morphology, 16S rRNA gene phylogenies, 16S–23S ITS rRNA region sequence dissimilarities, and phylogenomics. Four novel species of Roseofilum were isolated from benthic marine mats, three from the coasts of Florida, United States (R. capinflatum sp. nov., R. casamattae sp. nov., and R. acuticapitatum sp. nov.) and one from the coast of France (R. halophilum sp. nov.). Our analyses revealed that Roseofilum associated with coral BBD and those not associated with corals but rather from coastal benthic mats are systematically distinct based on both phylogenetic and phylogenomic analyses. Enzyme‐linked immunosorbent assay (ELISA) and LC–MS data indicated that microcystin production was found in one of the four species. [ABSTRACT FROM AUTHOR]

Previous studies have deciphered the genomic basis of host‐symbiont metabolic complementarity in vestimentiferans, bathymodioline mussels, vesicomyid clams and Alviniconcha snails, yet little is known about the chemosynthetic symbiosis in Thyasiridae—a family of Bivalvia regarded as an excellent model in chemosymbiosis research due to their wide distribution in both deep‐sea and shallow‐water habitats. We report the first circular thyasirid symbiont genome, named Candidatus Ruthturnera sp. Tsphm01, with a size of 1.53 Mb, 1521 coding genes and 100% completeness. Compared to its free‐living relatives, Ca. Ruthturnera sp. Tsphm01 genome is reduced, lacking components for chemotaxis, citric acid cycle and de novo biosynthesis of small molecules (e.g. amino acids and cofactors), indicating it is likely an obligate intracellular symbiont. Nevertheless, the symbiont retains complete genomic components of sulphur oxidation and assimilation of inorganic carbon, and these systems were highly and actively expressed. Moreover, the symbiont appears well‐adapted to anoxic environment, including capable of anaerobic respiration (i.e. reductions of DMSO and nitrate) and possession of a low oxygen‐adapted type of cytochrome c oxidase. Analysis of the host transcriptome revealed its metabolic complementarity to the incomplete metabolic pathways of the symbiont and the acquisition of nutrients from the symbiont via phagocytosis and exosome. By providing the first complete genome of reduced size in a thyasirid symbiont, this study enhances our understanding of the diversity of symbiosis that has enabled bivalves to thrive in chemosynthetic habitats. The resources will be widely used in phylogenetic, geographic and evolutionary studies of chemosynthetic bacteria and bivalves. [ABSTRACT FROM AUTHOR]

The analysis of meta-omics data requires the utilization of several bioinformatics tools and proficiency in informatics. The integration of multiple meta-omics data is even more challenging, and the outputs of existing bioinformatics solutions are not always easy to interpret. Here, we present a meta-omics bioinformatics pipeline, Meta-Omics Software for Community Analysis (MOSCA), which aims to overcome these limitations. MOSCA was initially developed for analysing metagenomics (MG) and metatranscriptomics (MT) data. Now, it also performs MG and metaproteomics (MP) integrated analysis, and MG/MT analysis was upgraded with an additional iterative binning step, metabolic pathways mapping, and several improvements regarding functional annotation and data visualization. MOSCA handles raw sequencing data and mass spectra and performs pre-processing, assembly, annotation, binning and differential gene/protein expression analysis. MOSCA shows taxonomic and functional analysis in large tables, performs metabolic pathways mapping, generates Krona plots and shows gene/protein expression results in heatmaps, improving omics data visualization. MOSCA is easily run from a single command while also providing a web interface (MOSGUITO). Relevant features include an extensive set of customization options, allowing tailored analyses to suit specific research objectives, and the ability to restart the pipeline from intermediary checkpoints using alternative configurations. Two case studies showcased MOSCA results, giving a complete view of the anaerobic microbial communities from anaerobic digesters and insights on the role of specific microorganisms. MOSCA represents a pivotal advancement in meta-omics research, offering an intuitive, comprehensive, and versatile solution for researchers seeking to unravel the intricate tapestry of microbial communities., (© 2024 John Wiley & Sons Ltd.)

Human microbiota assembly commences at birth, seeded by both maternal and environmental microorganisms. Ecological theory postulates that primary colonizers dictate microbial community assembly outcomes, yet such microbial priority effects in the human gut remain underexplored. Here using longitudinal faecal metagenomics, we characterized neonatal microbiota assembly for a cohort of 1,288 neonates from the UK. We show that the pioneering neonatal gut microbiota can be stratified into one of three distinct community states, each dominated by a single microbial species and influenced by clinical and host factors, such as maternal age, ethnicity and parity. A community state dominated by Enterococcus faecalis displayed stochastic microbiota assembly with persistent high pathogen loads into infancy. In contrast, community states dominated by Bifidobacterium, specifically B. longum and particularly B. breve, exhibited a stable assembly trajectory and long-term pathogen colonization resistance, probably due to strain-specific functional adaptions to a breast milk-rich neonatal diet. Consistent with our human cohort observation, B. breve demonstrated priority effects and conferred pathogen colonization resistance in a germ-free mouse model. Our findings solidify the crucial role of Bifidobacteria as primary colonizers in shaping the microbiota assembly and functions in early life., (© 2024. The Author(s).)

The rumen microbiome plays an important role in providing energy and protein to the host. Manipulation of rumen microbiome during early life may have a long-term beneficial effect on the health, growth performance, and feed efficiency of ruminants. To better understand the profiles and functional potentials of rumen microbiome in young ruminants, metagenomic binning was performed to investigate the rumen microbiome of goat kids from one to 84 days of age. A total of 797 metagenome-assembled genomes (MAGs) were recovered from the rumen of 42 Laiwu black goat kids. Our findings provide fundamental knowledge of the rumen microbiome during early life based on metagenomic binning, which may provide insights into effective strategies to achieve long-term beneficial effects on animal health and production., (© 2024. The Author(s).)

Methane is the second most abundant climate-active gas, and understanding its sources and sinks is an important endeavour in microbiology, biogeochemistry, and climate sciences 1,2 . For decades, it was thought that methanogenesis, the ability to conserve energy coupled to methane production, was taxonomically restricted to a metabolically specialized group of archaea, the Euryarchaeota 1 . The discovery of marker genes for anaerobic alkane cycling in metagenome-assembled genomes obtained from diverse habitats has led to the hypothesis that archaeal lineages outside the Euryarchaeota are also involved in methanogenesis 3-6 . Here we cultured Candidatus Methanosuratincola verstraetei strain LCB70, a member of the archaeal class Methanomethylicia (formerly Verstraetearchaeota) within the phylum Thermoproteota, from a terrestrial hot spring. Growth experiments combined with activity assays, stable isotope tracing, and genomic and transcriptomic analyses demonstrated that this thermophilic archaeon grows by means of methyl-reducing hydrogenotrophic methanogenesis. Cryo-electron tomography revealed that Ca. M. verstraetei are coccoid cells with archaella and chemoreceptor arrays, and that they can form intercellular bridges connecting two to three cells with continuous cytoplasm and S-layer. The wide environmental distribution of Ca. M. verstraetei suggests that they might play important and hitherto overlooked roles in carbon cycling within diverse anoxic habitats., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)