Global Distribution Patterns and Pangenomic Diversity of the Candidate Phylum "Latescibacteria" (WS3)

The application of varying amount of green manure combined with nitrogen fertilizer altered the soil bacterial community and rice yield in karst paddy areas

Long-term application of green manure (GM) and nitrogen (N) fertilizers markedly improved soil fertility and boosted rice yield in ecologically fragile karst paddy fields. However, the precise response mechanisms of the soil bacterial community to varying amounts of green manure alone and in combination with N fertilizer in such environments remain poorly elucidated. In this study, we investigated the soil bacterial communities, keystone taxa, and their relationship with soil environmental variables across eight fertilization treatments. These treatments included group without N addition (N0M0, no N fertilizer and no GM; N0M22.5, 22.5 t/ha GM; N0M45, 45 t/ha GM, N0M67.5, 67.5 t/ha GM) and group with N addition (NM0, N fertilizer and no GM; NM22.5, N fertilizer and 22.5 t/ha GM; NM45, N fertilizer and 45 t/ha GM; NM67.5, N fertilizer and 67.5 t/ha GM). The results revealed that increasing green manure input significantly boosted rice yield by 15.51-22.08% and 21.84-35% in both the group without and with N addition, respectively, compared to N0M0 treatment. Moreover, with escalating green manure input, soil TN, AN, AK, and AP showed an increasing trend in the group without N addition. However, following the addition of N fertilizer, TN and AN content initially rose, followed by a decline due to the enhanced nutrient availability for rice. Furthermore, the application of a large amount of N fertilizer decreased the C: N ratio in the soil, resulting in significant changes in both the soil microbial community and its function. Particularly noteworthy was the transition of keystone taxa from their original roles as N-fixing and carbon-degrading groups (oligotrophs) to roles in carbon degradation (copiotrophs), nitrification, and denitrification. This shift in soil community and function might serve as a primary factor contributing to enhanced nutrient utilization efficiency in rice, thus significantly promoting rice yield.

Response of sediment microbial communities to the flow effect of the triangular artificial reef: A simulation-based experimental study

Artificial reefs (ARs), as an important tool for habitat restoration, play significant impacts on benthic microbial ecosystems. This study utilized 16S rRNA gene sequencing technology and computational fluid dynamics (CFD) flow simulation to investigate the effects of flow field distribution around ARs on microbial community structure. The results revealed distinct regional distribution patterns of microbial communities affected by different hydrodynamic conditions. Flow velocity and flow regime of water in sediment-water interface shaped the microbial community structure. The diversity and richness in R-HF were significantly decreased compared to other five regions (p < 0.05). At the phyla and OUT levels, most abundant taxa (1>%) showed an enrichment trend in R-HB. However, more than half of differentially abundant taxa were enriched in R-HB, which was significantly correlated with organic matter (OM). Bugbase phenotypic predictions indicated a low abundance of the anaerobic phenotype in R-HF and a high abundance of the biofilm-forming phenotype in R-HB.

Anammox process in anaerobic baffled biofilm reactors with columnar packings: Characteristics of flow field and microbial community

The enrichment of anammox bacteria is a key issue in the application of anammox processes. A new type of reactor － anaerobic baffle biofilm reactor (ABBR) developed from anaerobic baffle reactor (ABR) was filled with columnar packings and established for effective enrichment of anammox bacteria. The flow field analysis showed that, compared with ABR, ABBR narrowed the dead zone so as to improve the substrate transferring performances. Two ABBRs with different types of columnar packings (Packings 1 and Packings 2) were constructed to culture anammox biofilms. Packings 1 consisted of the single-form honeycomb carriers while Packings 2 was modular composite packings consisting of non-woven fabric and honeycomb carriers. The effects of different types of columnar packings on microbial community and nitrogen removal were studied. The ABBR filled with Packings 2 had a higher retention rate of biomass than the ABBR filled with Packings 1, making the anammox start-up period be shortened by 21.28%. The enrichment of anammox bacteria were achieved and the dominant anammox bacteria were Candidatus Brocadia in both R1 and R2. However, there were four genera of anammox bacteria in R2 and one genus of anammox bacteria in R1, and the cell density of anammox bacteria in R2 was 95% higher than that in R1. R2 has the advantage of maintaining excellent and stable nitrogen removal performance at high nitrogen loading rate. The results revealed that the packings composed of two types of carriers may have a better enrichment effect on anammox bacteria. This study is of great significance for the rapid enrichment of anammox bacteria and the technical promotion of anammox process.

Diversity and plant growth promoting ability of rice root-associated bacteria in Burkina-Faso and cross-comparison with metabarcoding data

Plant-associated bacteria are essential partners in plant health and development. In addition to taking advantage of the rapid advances recently achieved in high-throughput sequencing approaches, studies on plant-microbiome interactions require experiments with culturable bacteria. A study on the rice root microbiome was recently initiated in Burkina Faso. As a follow up, the aim of the present study was to develop a collection of corresponding rice root-associated bacteria covering maximum diversity, to assess the diversity of the obtained isolates based on the culture medium used, and to describe the taxonomy, phenotype and abundance of selected isolates in the rice microbiome. More than 3,000 isolates were obtained using five culture media (TSA, NGN, NFb, PCAT, Baz). The 16S rRNA fragment sequencing of 1,013 selected isolates showed that our working collection covered four bacterial phyla (Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes) and represented 33% of the previously described diversity of the rice root microbiome at the order level. Phenotypic in vitro analysis of the plant growth promoting capacity of the isolates revealed an overall ammonium production and auxin biosynthesis capacity, while siderophore production and phosphate solubilisation were enriched in Burkholderia, Ralstonia, Acinetobacter and Pseudomonas species. Of 45 representative isolates screened for growth promotion on seedlings of two rice cultivars, five showed an ability to improve the growth of both cultivars, while five others were effective on only one cultivar. The best results were obtained with Pseudomonas taiwanensis ABIP 2315 and Azorhizobium caulinodans ABIP 1219, which increased seedling growth by 158% and 47%, respectively. Among the 14 best performing isolates, eight appeared to be abundant in the rice root microbiome dataset from previous study. The findings of this research contribute to the in vitro and in planta PGP capacities description of rice root-associated bacteria and their potential importance for plants by providing, for the first time, insight into their prevalence in the rice root microbiome.

The evolution of nitrogen transformation microorganism consortium under continued manganese domestication conditions

Manganese redox-stimulated bioremediation of nitrogen wastewater is receiving increasing attention. However, the nitrogen metabolic capacity and community evolution during manganese-mediated nitrogen transformation process under continued manganese domestication conditions are ambiguous. In this study, nitrogen- metabolizing microbial consortiums were incubated with synthesized Mn-humic acid complex (Mn-HA) for one month (M1), three months (M2) and six months (M3), respectively. During the Mn-HA incubation period, Bio-MnOx accompanying with bacterial consortiums (MnOB consortiums) with high TIN removal capacities were obtained. The TIN removal rates in M1, M2 and M3 were 0.220, 1.246 and 4.237 mg·L-1·h-1, respectively, which were 15.961, 90.006 and 1550.006 times higher than CK (Control Check group, no Mn-HA added group) (0.014 mg·L-1·h-1), respectively. Functional genes (amoA, AMX and narG) were most abundant in M3, which was associated with the highest nitrogen removal rate in M3. MnOB1 (bacterial consortium in M1), including Geobactor, Geothrix, Anaeromyxobacter and Bacillus, may be responsible for the Mnammox-NDMO (MnOx reduction coupled to ammonium oxidation - nitrate/nitrite-dependent low-valent Mn oxidation) process. MnOB3 (bacterial consortium in M2) enriched nitrifying bacteria Ellin6067, and denitrifying bacteria Denitratisoma, which dominated nitrogen transformation. MnOB6 (bacterial consortium in M3) enriched denitrifiers Denitratisoma, nitrifiers Ellin6067 and potential anammox bacteria SM1A02, Candidatus_Brocadia. Combined with the reduced abundance of Nitrospirae, a short-cut partial nitrification and denitrification (PND) or partial nitrification, denitrification and anammox (PNDA) could occurred in M2 and M3. It is suggested that community may have evolved into an energetically efficient short-cut nitrification, denitrification and anammox consortium to replace the full-range nitrification and denitrification community in M1 and CK under the continued manganese domestication conditions. Enhanced metabolic pathways of hydroxylamine oxidation and the nitric oxide reduction may confirm that PND or PNDA occurred in M2 and M3.

Co-exposure of dimethomorph and imidacloprid: effects on soil bacterial communities in vineyard soil

In Taiwan, the pesticides dimethomorph and imidacloprid are recommended for pest control in vineyards. Therefore, tank-mixing of these two pesticides is usually a routine practice before application. This study analyzed the influence of vineyard soil microbial flora under the recommended and high dosages (100 times the recommended dosage) of dimethomorph and imidacloprid. Individual and combined applications of pesticides were also tested through batches of soil incubation experiments. Four treatments-control (C), dimethomorph (DT), imidacloprid (IM), and mixed application of dimethomorph and imidacloprid (ID)-were used in the experimental design. From the soil metabolism, no significant reaction was observed after 2 months in the recommended dosage group, regardless of whether the pesticides were being applied individually or combined. For the high dosage, imidacloprid showed a higher effect than the co-exposure treatments, showing a possible prolonged effect after its repetitive application. From PCoA analysis, pesticide treatments altered the soil ecology after 2 months, and the effect of imidacloprid can be explicitly observed at high dosages. At the phylum level, Acidobacteria can indicate pesticide application around the recommended dosage. It was inhibited by ID on day 7 and was augmented by all pesticides on day 63. The effect of the recommended dosage of pesticide mixtures after 2 months of incubation was revealed in the minor families Gemmataceae and Pirellulaceae, while the high dosage treatments affected both the core and the minor families. Our findings verified the changes in the composition of microbial communities upon pesticide application, which would affect carbon, nitrogen, sulfur, phosphorous cycles, and contaminant removal ability within the vineyard.

Microbe-driven elemental cycling enables microbial adaptation to deep-sea ferromanganese nodule sediment fields

BACKGROUND

Ferromanganese nodule-bearing deep-sea sediments cover vast areas of the ocean floor, representing a distinctive habitat in the abyss. These sediments harbor unique conditions characterized by high iron concentration and low degradable nutrient levels, which pose challenges to the survival and growth of most microorganisms. While the microbial diversity in ferromanganese nodule-associated sediments has been surveyed several times, little is known about the functional capacities of the communities adapted to these unique habitats.

RESULTS

Seven sediment samples collected adjacent to ferromanganese nodules from the Clarion-Clipperton Fracture Zone (CCFZ) in the eastern Pacific Ocean were subjected to metagenomic analysis. As a result, 179 high-quality metagenome-assembled genomes (MAGs) were reconstructed and assigned to 21 bacterial phyla and 1 archaeal phylum, with 88.8% of the MAGs remaining unclassified at the species level. The main mechanisms of resistance to heavy metals for microorganisms in sediments included oxidation (Mn), reduction (Cr and Hg), efflux (Pb), synergy of reduction and efflux (As), and synergy of oxidation and efflux (Cu). Iron, which had the highest content among all metallic elements, may occur mainly as Fe(III) that potentially functioned as an electron acceptor. We found that microorganisms with a diverse array of CAZymes did not exhibit higher community abundance. Instead, microorganisms mainly obtained energy from oxidation of metal (e.g., Mn(II)) and sulfur compounds using oxygen or nitrate as an electron acceptor. Chemolithoautotrophic organisms (Thaumarchaeota and Nitrospirota phyla) were found to be potential manganese oxidizers. The functional profile analysis of the dominant microorganisms further indicated that utilization of inorganic nutrients by redox reactions (rather than organic nutrient metabolism) is a major adaptive strategy used by microorganisms to support their survival in the ferromanganese nodule sediments.

CONCLUSIONS

This study provides a comprehensive metagenomic analysis of microbes inhabiting metal-rich ferromanganese nodule sediments. Our results reveal extensive redundancy across taxa for pathways of metal resistance and transformation, the highly diverse mechanisms used by microbes to obtain nutrition, and their participation in various element cycles in these unique environments. Video Abstract.

Effects of Degradation on Microbial Communities of an Amazonian Mangrove

Mangroves provide a unique ecological environment for complex microbial communities, which play important roles in biogeochemical cycles, such as those for carbon, sulfur, and nitrogen. Microbial diversity analyses of these ecosystems help us understand the changes caused by external influences. Amazonian mangroves occupy an area of 9000 km², corresponding to 70% of the mangroves in Brazil, on which studies of microbial biodiversity are extremely scarce. The present study aimed to determine changes in microbial community structure along the PA-458 highway, which fragmented a mangrove zone. Mangrove samples were collected from three zones, (i) degraded, (ii) in the process of recovery, and (iii) preserved. Total DNA was extracted and submitted for 16S rDNA amplification and sequencing on an MiSeq platform. Subsequently, reads were processed for quality control and biodiversity analyses. The most abundant phyla were Proteobacteria, Firmicutes, and Bacteroidetes in all three mangrove locations, but in significantly different proportions. We observed a considerable reduction in diversity in the degraded zone. Important genera involved in sulfur, carbon, and nitrogen metabolism were absent or dramatically reduced in this zone. Our results show that human impact in the mangrove areas, caused by the construction of the PA-458 highway, has resulted in a loss of biodiversity.

The greenhouse effect of antibiotics: The influence pathways of antibiotics on methane release from freshwater sediment

The impact of antibiotics on methane (CH₄) release from sediment involves both CH₄ production and consumption processes. However, most relevant studies lack a discussion of the pathways by which antibiotics affect CH₄ release and do not highlight the role played by the sediment chemical environment in this influence mechanism. Here, we collected field surface sediments and grouped them with various antibiotic combination concentration gradients (50, 100, 500, 1000 ng g^-1) under a 35-day indoor anaerobic constant temperature incubation. We found that the positive effect of antibiotics on sediment CH₄ release potential appeared later than the positive effect on sediment CH₄ release flux. Still, the positive effect of high-concentration antibiotics (500, 1000 ng g^-1) occurred with a lag in both processes. Also, the positive effect of high-concentration antibiotics was significantly higher than low-concentration antibiotics (50, 100 ng g^-1) in the later incubation period (p < 0.05). We performed a multi-collinearity assessment of sediment biochemical indicators, followed by a generalized linear model with negative binomial regression (GLM-NB) to obtain essential variables. In particular, we conducted the interaction analysis on CH₄ release potential and flux regression for the influence pathways construction. The partial least-squares path modeling (PLS-PM) demonstrated that the positive effect of antibiotics on CH₄ release (Total effect = 0.2579) was primarily attributed to their effect on the sediment chemical environment (Direct effect = 0.5107). These findings greatly expand our understanding of the antibiotic greenhouse effect in freshwater sediment. Further studies should more carefully consider the effects of antibiotics on the sediment chemical environment, and continuously improve the mechanistic studies of antibiotics on sediment CH₄ release.

Response of methanogenic system to long-term polycyclic aromatic hydrocarbon exposure: Adsorption and biodegradation, performance variation, and microbial function assessment

Phenanthrene (PHE) as a typical polycyclic aromatic hydrocarbon (PAH) is prevalent and harmful to organisms in petroleum-polluted sites. The effects of PHE concentration levels on performance, microbial community and functions in methanogenic system were comprehensively investigated by an operation of UASB reactor (198 days) and a series of batch tests. The results found that PHE was prone to accumulate in reactor by sludge adsorption (Final concentration = 12.53 mg/g TS Sludge), which posed significant influences on methanogenic system. The removal of chemical oxygen demand (COD), NH₄⁺-N and volatile fatty acids (VFAs) in reactor were reduced with PHE accumulation. Meanwhile, microbes with higher ATPase secrete more EPS activity to self-protect against PHE toxicity. Sequencing analysis showed that PHE interfered significantly diversity and structure of microbial community. For bacteria, PHE was toxic to Bacteroidetes and Latescibacteria, while syntrophs (f_Syntrophaceae, Syntrophorhabdus, etc.) involved in VFAs oxidation and aromatic organics degradation were tolerant of PHE stress. For archaea, acetoclastic methanogens (Methanosaeta) abundance was continuously diminished by 45.1% under long-term PHE exposure. Further functions analysis suggested that microbial community accelerated amino acid metabolism, energy metabolism and xenobiotics biodegradation & metabolism to satisfy physiological demanding under PHE stress. Combining batch tests of methanogenic metabolism proved that acetoclastic methanogenesis was negatively affected by PHE due to inhibition of functional enzymes (acetate kinase, phosphate acetyltransferase, etc.) expression. These findings may provide the basis for enhancing bioremediation of PAH pollution in anaerobic environment.

Water microecology is affected by seasons but not sediments: A spatiotemporal dynamics survey of bacterial community composition in Lake Changshou-The largest artificial lake in southwest China

This study aimed to evaluate the correlation between microecology of sediments and water as well as their spatial-temporal variations in Changshou Lake. The results demonstrated that microecology in the lake exhibits spatiotemporal heterogeneity, and microbial diversity of sediments was significantly higher than that of water body. Further, it was found that there was statistically insignificant positive correlation between microecology of sediments and that of water body. PCoA and community structure analysis revealed that the predominant phyla which exhibited significant spatial differences in sediments were Proteobacteria, Actinobacteria and Planctomycetes. While, the distribution of dominant bacteria Actinobacteria and Verrucomicrobia in water body showed significant seasonal differences. Microbial networks analysis indicated that there was a cooperative symbiotic relationship between lake microbial communities. Notably, the same bacterial genus had no significant positive correlation in sediment and water, which suggested that bacteria transport between sediment-water interface does not influence the microecological functions of lake water.

Ecological life strategies of microbes in response to antibiotics as a driving factor in soils

Antibiotics as a selection pressure driving the evolution of soil microbial communities is not well understood. Since microbial functions govern ecosystem services, an ecological framework is required to understand and predict antibiotic-induced functional and structural changes in microbial communities. Therefore, metagenomic studies explaining the impacts of antibiotics on soil microbial communities were mined, and alterations in microbial taxa were analyzed through an ecological lens using Grimes's Competitor-Stress tolerator-Ruderal (CSR) model. We propose considering antibiotics as the primary abiotic factor mentioned in the CSR model and classifying non-susceptible microbial taxa as degraders, resistant, and resilient groups analogous to competitors, stress tolerators, and ruderal strategists, respectively. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were among the phyla harboring most members with antibiotic-resistant groups. However, some antibiotic-resistant microbes in these phyla could not only tolerate but also subsist solely on antibiotics, while others degraded antibiotics as a part of secondary metabolism. Irrespective of their taxonomic affiliation, microbes with each life strategy displayed similar phenotypic characteristics. Therefore, it is recommended to consider microbial functional traits associated with each life strategy while analyzing the ecological impacts of antibiotics. Also, potential ecological crises posed by antibiotics through changes in microbial community and ecosystem functions were visualized. Applying ecological theory to understand and predict antibiotics-induced changes in microbial communities will also provide better insight into microbial behavior in the background of emerging contaminants and help develop a robust ecological classification system of microbes.

Metagenomics and metatranscriptomics reveal broadly distributed, active, novel methanotrophs in the Gulf of Mexico hypoxic zone and in the marine water column

The northern Gulf of Mexico (nGOM) hypoxic zone is a shallow water environment where methane, a potent greenhouse gas, fluxes from sediments to bottom water and remains trapped due to summertime stratification. When the water column is destratified, an active planktonic methanotrophic community could mitigate the efflux of methane, which accumulates to high concentrations, to the atmosphere. To investigate the possibility of such a biofilter in the nGOM hypoxic zone we performed metagenome assembly, and metagenomic and metatranscriptomic read mapping. Methane monooxygenase (pmoA) was an abundant transcript, yet few canonical methanotrophs have been reported in this environment, suggesting a role for non-canonical methanotrophs. To determine the identity of these methanotrophs, we reconstructed six novel metagenome-assembled genomes (MAGs) in the Planctomycetota, Verrucomicrobiota and one putative Latescibacterota, each with at least one pmoA gene copy. Based on ribosomal protein phylogeny, closely related microbes (mostly from Tara Oceans) and isolate genomes were selected and co-analyzed with the nGOM MAGs. Gene annotation and read mapping suggested that there is a large, diverse and unrecognized community of active aerobic methanotrophs in the nGOM hypoxic zone and in the global ocean that could mitigate methane flux to the atmosphere.

Comparison of environmental microbiomes in an antibiotic resistance-polluted urban river highlights periphyton and fish gut communities as reservoirs of concern

Natural waterways near urban areas are heavily impacted by anthropogenic activities, including their microbial communities. A contaminant of growing public health concern in rivers is antibiotic resistant genes (ARGs), which can spread between neighboring bacteria and increase the potential for transmission of AR bacteria to animals and humans. To identify the matrices of most concern for AR, we compared ARG burdens and microbial community structures between sample types from the Scioto River Watershed, Ohio, the United States, from 2017 to 2018. Five environmental matrices (water, sediment, periphyton, detritus, and fish gut) were collected from 26 river sites. Due to our focus on clinically relevant ARGs, three carbapenem resistance genes (bla_KPC, bla_NDM, and bla_OXA-48) were quantified via DropletDigital™ PCR. At a subset of nine urbanized sites, we conducted16S rRNA gene sequencing and functional gene predictions. Carbapenem resistance genes were quantified from all matrices, with bla_KPC being the most detected (88 % of samples), followed by bla_NDM (64 %) and bla_OXA-48 (23 %). Fish gut samples showed higher concentrations of bla_KPC and bla_NDM than any other matrix, indicating potential ARG bioaccumulation, and risk of broader dissemination through aquatic and nearshore food webs. Periphyton had higher concentrations of bla_NDM than water, sediment, or detritus. Microbial community analysis identified differences by sample type in community diversity and structure. Sediment samples had the most diverse microbial communities, and detritus, the least. Spearman correlations did not reveal significant relationships between the concentrations of the monitored ARGs and microbial community diversity. However, several differentially abundant taxa and microbial functions were identified by sample type that is definitive of these matrices' roles in the river ecosystem and habitat type. In summary, the fish gut and periphyton are a concern as AR reservoirs due to their relatively high concentration of carbapenem resistance genes, diverse microbial communities, and natural functions that promote AR.

Agricultural soil physico-chemical parameters and microbial abundance and diversity under long-run farming practices: A greenhouse study

The growth of agriculture led to indiscriminate use of synthetic pesticides or fertilizers and unsustainable crop management farming practices which can aggravate harmful impacts on the microbial population and physical and chemical characteristics of soil ecosystem. Based on this fact, the present study was planned to evaluate the effect of long run farming practices on different soil physico-chemical parameters and soil microbial abundance and diversity within different soil depth (0–20 cm and 20–40 cm) at Quzhou Experimental Station of China Agricultural University, Hebei, China during October and December, 2016. The effect of farming practices on soil microbial abundance and diversity was studied by phospho-lipid fatty acid (PLFA) and DNA high-throughput sequencing methods. The findings revealed that soil is neutral to slightly alkaline in nature with highest water content under organic farming (ORF) at 0–20 cm and least under conventional farming at 20–40 cm depth. It was found that the ORF significantly increased the contents of total organic carbon (TOC), total carbon (TC), ammonium nitrogen, available nitrogen (AN), total nitrogen (TN), total phosphorus (TP), and available phosphorus (AP) followed by low input and conventional farming modes in both October and December soil samples. The correlation analysis showed significantly (at p ≤ 0.05 and 0.01) strong positive relationship within different physical and chemical properties of the soil under study. ANOVA and MANOVA analysis indicated significant effect of interaction between soil depth and farming modes on soil parameters. PCA analysis showed the most significant correlation between most of the bacterial types (G + bacteria, G− bacteria, actinomycetes) and soil AP, total available nitrogen, TOC and soil WC. Pearson correlation analysis revealed a significant correlation between microbial phylum groups (Proteobacteria, Bacteroidetes, and Latescibacteria) and microbial class group (Alphaproteobacteria, Sphingobacteriia, Flavobacteriia) with most of the soil physicochemical properties.

Plant roots send metabolic signals to microbes in response to long-term overgrazing

Overgrazing directly and indirectly affects soil microorganisms, which can have feedback effects on plant growth. Little is known about the root metabolites plants produce and whether they recruit beneficial microbes in response to overgrazing. Here, we used the dominant grassland species Leymus chinensis to explore correlations between root metabolites and the rhizosphere microbiome shaped by long-term overgrazing, which was determined by using LC-MS technology and high-throughput sequencing. In total, 839 metabolites were detected, with 41 significantly higher and 3 significantly lower in overgrazing versus grazing exclusion plots. The rhizosphere bacterial community was changed, but the fungal community was not altered. Moreover, 11 bacterial orders were found only in the overgrazed samples, and these showed close relationships to root metabolites and certain soil properties. Of these, Latescibacterales, B10-SB3A, and Nitrosococcales are known to be involved in growth promotion, C and N metabolism, respectively. In addition, root metabolites play an important role in mediating root-fungi interactions. The beneficial fungal orders Agaricales and Sordariales have a tread to be higher maybe due to root metabolites, mainly facilitate nutrient absorption and protect organic carbon in the soil, respectively. Our results indicate that grassland plants send metabolic signals to recruit key beneficial bacteria and stabilize fungal communities to alleviate grazing-induced stress in typical grassland ecosystems.

Soil Metabolomics Predict Microbial Taxa as Biomarkers of Moisture Status in Soils from a Tidal Wetland

We present observations from a laboratory-controlled study on the impacts of extreme wetting and drying on a wetland soil microbiome. Our approach was to experimentally challenge the soil microbiome to understand impacts on anaerobic carbon cycling processes as the system transitions from dryness to saturation and vice-versa. Specifically, we tested for impacts on stress responses related to shifts from wet to drought conditions. We used a combination of high-resolution data for small organic chemical compounds (metabolites) and biological (community structure based on 16S rRNA gene sequencing) features. Using a robust correlation-independent data approach, we further tested the predictive power of soil metabolites for the presence or absence of taxa. Here, we demonstrate that taking an untargeted, multidimensional data approach to the interpretation of metabolomics has the potential to indicate the causative pathways selecting for the observed bacterial community structure in soils.

Elucidating the role of extracellular polymeric substances (EPS) in dewaterability of fecal sludge from onsite sanitation systems, and changes during anaerobic storage

As the importance of fecal sludge management (FSM) is increasingly being realized, the need for adequately designed and functioning fecal sludge (FS) treatment plants is also increasing. Research to fill this gap is only emerging and dewatering is a key challenge for developing sustainable treatment solutions. This study evaluated the effect of extracellular polymeric substances (EPS) on dewaterability of FS, and how EPS and dewaterability change during anaerobic storage (as a proxy for time in onsite containment). EPS was extracted from FS and activated sludge using Na₂CO₃ and sonication and added to sludge samples to determine the effect on dewaterability. The results confirmed that an increase in EPS had a direct impact of decreasing FS dewaterability (as capillary suction time). In this context, we evaluated FS degradation during anaerobic storage, the effect of anaerobic storage time on EPS, EPS fractions and particle size distribution, and the effect of variations in these factors on FS dewaterability. Variations in EPS, EPS fraction and particle size distribution during anaerobic storage were less than expected and average VS reduction of 20% was recorded over 7 weeks. Although anaerobic digestion was verified (biogas production), the results indicate that kinetics of degradation of FS is different from wastewater sludges. Comparatively, EPS fractions in FS were 70 - 75% lower and with higher fractions of humic-like substances than wastewater sludges. Although EPS significantly affects FS dewaterability, anaerobic storage time is not a predictor of dewaterability.

The parameters determining hyperaccumulator rhizobacteria diversity depend on the study scale

Soils harbor some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. Numerous parameters, intrinsic to plant physiology, life history and the soil itself, can influence the structure of rhizomicrobial communities. While our knowledge of rhizosphere microbial diversity is increasing, opinion is divided as to whether the factors that most impact this diversity are abiotic, climatic or plant selection. Here we focused on the rhizosphere bacterial diversity of nickel hyperaccumulator plants (28 species from Mediterranean or tropical climates). We showed, by leveraging 16S Illumina sequencing of 153 ultramafic rhizosphere soils, that bacterial genetic diversity was highest in Mediterranean habitats where plant diversity was the lowest. Concerning those parameters driving this diversity, we demonstrated that climate drives bacterial diversity, in particular with the annual temperature variation. Focusing on each region, we underlined the substantial role of soil physicochemical parameters. Our results highlight the importance of considering spatial scale when explaining bacterial community diversity.

The Shift of Soil Bacterial Community After Afforestation Influence Soil Organic Carbon and Aggregate Stability in Karst Region

Soil microbes regulate the carbon cycle and affect the formation and stabilization of soil aggregates. However, the interactions between the soil microbial community and soil organic carbon (SOC) fractions, organic carbon (OC) content in aggregates, and soil aggregate stability after afforestation are remain poorly understood. In our study, we investigated SOC fractions in bulk soil, aggregate-associated OC content, soil aggregate stability, and soil bacterial community with high-throughput 16S rRNA sequencing at sites representing natural secondary forest (NF) and managed forest (MF), with cropland (CL) as reference in a degraded karst region of Southwest China. Our results showed that afforestation remarkably increased the SOC fraction and OC content in aggregates, the mean weight diameter (MWD), and the mean geometric diameter (GMD). The most dominant bacterial phyla detected were Acidobacteriota, Actinobacteriota, Proteobacteria, and Chloroflexi across all soils. Afforestation remarkably altered the relative abundances of most of the dominant soil bacteria at the phylum, class, and order levels. Interestingly, such changes in the abundance of soil bacteria taxa had significantly effects on SOC fraction, aggregate-associated OC content, MWD, and MGD. The abundance of dominant bacterial taxa such as Methylomirabilota, Latescibacterota, Methylomirabilia, MB-A2-108, norank_Latescibacterota; Dehalococcoidia, Rokubacteriales, Gaiellales, Microtrichales, norank_c__MB-A2-108, norank_c__norank_p__Latescibacterota, Rhizobiales, and S085 not only remarkably increased but also had significant positive effects on SOC fractions and aggregate-associated OC content after afforestation. Moreover, MWD and MGD were positively correlated with the relative abundance of Methylomirabilota, Methylomirabilia, Rokubacteriales, Latescibacterota, and Rhizobiales. Results indicated the importance of certain soil bacteria for regulating SOC storage and soil aggregate stability. We concluded that afforestation on cropland could alter the abundance of soil bacteria, and these changes modulate the stability of soil aggregates and SOC fractions.

Microbial communities in sandy beaches from the three domains of life differ by microhabitat and intertidal location

The microbial communities of sandy beaches are poorly described despite the biogeochemical importance and ubiquity of these ecosystems. Using metabarcoding of the 16S and 18S rRNA genes, we investigated the diversity, microhabitats (with or between sand grains), and intertidal distributions of microorganisms (including meiofauna) from pristine sandy beaches in British Columbia, Canada, and hypothesized that abiotic variations due to microhabitat or intertidal gradients influences the distribution of microorganisms on local scales. Bacterial, archaeal, and protistan communities of the sand were clearly distinct from interstitial communities, and from planktonic communities of the overlying seawater, which correlated with differences in function and lifestyle, e.g., sulfur reduction and gliding motility. In contrast, meiofaunal communities could not be distinguished by sample type, suggesting that they are more frequently mobilized between these microhabitats. Across intertidal zones, high intertidal, mid intertidal, and low intertidal/swash communities were distinct and correlated with moisture, organic carbon and phosphate content, implying that the distribution of microorganisms is influenced by intertidal abiotic gradients. However, few taxa at the genus or species level individually contributed to this zonation pattern; rather, a unique combination of multiple microbial taxa was more likely responsible. Although significant differences in microbial community composition on sandy beaches can be attributed to microhabitat and intertidal gradients, further investigations are needed to assess community assembly processes, the consistency of these distributions, and the functions of the majority of the microorganisms observed in the sand and their effects on the biogeochemistry and ecology of sandy beaches.

Effects of dietary fiber on intestinal microbiota in geese evaluated by 16SrRNA gene sequencing

AIMS

The purpose of the research is to study the effects of different fiber types and sources on the intestinal flora of geese.

METHODS AND RESULTS

A total of 48 geese (males 35 days old) were divided into 4 groups, each of which included 3 replicates of 4 geese. Groups 1 to 4 were fed a diet containing 5% corn stover Crude fiber (CF, the LJ group), 8% corn stover CF (the HJ group), 5% alfalfa CF (the LM group), or 8% alfalfa CF (the HM group) respectively. After 42 days of feeding, the intestinal flora of each group was determined by 16SrRNA gene sequencing. In the duodenum, the diet supplemented with corn stover meal increased the relative abundance of Proteobacteria, Actinobacteria and Euryarchaeota, and with alfalfa as fiber source increased the relative abundance of Firmicutes, Bacteroidetes, Tenericutes and Chloroflexi. In the jejunum, Bacteroidetes, Actinobacteria, Planctomycetes, Acidobacteria, Tenericutes and Spirochetes were significantly more abundant in the corn stover group. There were no significant differences among the results for the other two fiber sources, which were fibre level in their influence where in ileum. Firmicutes, Deferribacteres and Euryarchaeota with corn stover as fiber source in the cecum were higher than the alfalfa group.

CONCLUSIONS

Different fiber sources have significant effects on goose gut microbiota. There were same flora has the same trend of change in different intestinal segments. The relative fiber source in the ileum makes the gut microbiota more sensitive to differences in fiber levels..

SIGNIFICANCE AND IMPACT OF THE STUDY

This study proved that the dietary fibre affects the intestinal flora. At the same time, different groups of dietary fibre may be used to provide the possibility to study functional roles of specific bacteria in host physiology.

Diversity and distribution of sediment bacteria across an ecological and trophic gradient

The microbial communities of lake sediments have the potential to serve as valuable bioindicators and integrators of watershed land-use and water quality; however, the relative sensitivity of these communities to physio-chemical and geographical parameters must be demonstrated at taxonomic resolutions that are feasible by current sequencing and bioinformatic approaches. The geologically diverse and lake-rich state of Minnesota (USA) is uniquely situated to address this potential because of its variability in ecological region, lake type, and watershed land-use. In this study, we selected twenty lakes with varying physio-chemical properties across four ecological regions of Minnesota. Our objectives were to (i) evaluate the diversity and composition of the bacterial community at the sediment-water interface and (ii) determine how lake location and watershed land-use impact aqueous chemistry and influence bacterial community structure. Our 16S rRNA amplicon data from lake sediment cores, at two depth intervals, data indicate that sediment communities are more likely to cluster by ecological region rather than any individual lake properties (e.g., trophic status, total phosphorous concentration, lake depth). However, composition is tied to a given lake, wherein samples from the same core were more alike than samples collected at similar depths across lakes. Our results illustrate the diversity within lake sediment microbial communities and provide insight into relationships between taxonomy, physicochemical, and geographic properties of north temperate lakes.

Mangrove microbiota along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America): Drivers and potential bioindicators

The microbial communities inhabiting the Atlantic-East Pacific (AEP) mangroves have been poorly studied, and mostly comprise chronically polluted mangroves. In this study, we characterized changes in the structure and diversity of microbial communities of mangroves along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America) that experience low human impact. The microbial communities were assigned into 50 phyla. Proteobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, and Planctomycetes were the most abundant taxa. The environmental determinants found to significantly correlated to the microbial communities at these mangroves were granulometry, dieldrin concentration, pH, and total carbon (TC) content. Furthermore, a precise analysis of the sediment highlights the existence of three types of anthropogenic pressure among the stations: (i) organic matter (OM) enrichment due to the proximity to the city and its wastewater treatment plant, (ii) dieldrin contamination, and (iii) naphthalene contamination. These forms of weak anthropogenic pressure seemed to impact the bacterial population size and microbial assemblages. A decrease in Bathyarchaeota, "Candidatus Nitrosopumilus", and Nitrospira genera was observed in mangroves subjected to OM enrichment. Mangroves polluted with organic contaminants were enriched in Desulfobacteraceae, Desulfarculaceae, and Acanthopleuribacteraceae (with dieldrin or polychlorobiphenyl contamination), and Chitinophagaceae and Geobacteraceae (with naphthalene contamination). These findings provide insights into the main environmental factors shaping microbial communities of mangroves in the AEP that experience low human impact and allow for the identification of several potential microbial bioindicators of weak anthropogenic pressure.

Sediment and their bacterial communities in an industrialized estuary after Hurricane Harvey

Estuaries experience variable physicochemical conditions, especially after hurricanes and due to anthropogenic sources of pollution. Their microbial communities are not as well understood in terms of community structure and diversity, particularly in response to stresses from pollution and severe events. This study presents a 16S rRNA-based description of sediment microbial communities in the Houston Ship Channel-Galveston Bay estuary after Hurricane Harvey in 2017. A total of 11 sites were sampled, and microbial genomic DNA was isolated from sediment. The presence and abundance of specific bacterial and archaeal taxa in the sediment indicated pollutant inputs from identified legacy sources. The abundance of certain microbial groups was explained by the mobilization of contaminated sediment and sediment transport due to Harvey. Several microorganisms involved in the biodegradation of xenobiotics were observed. The spatial occurrence of Dehalococcoidia, a degrader of persistent polychlorinated compounds, was explained in relation to sediment properties and contaminant concentrations.

Longitudinal patterns in sediment type and quality during daily flow regimes and following natural hazards in an urban estuary: a Hurricane Harvey retrospective

Understanding the transport of sediments in urban estuaries and their effects on water quality and microorganisms is a convergent challenge that has yet to be addressed especially as a result of natural hazards that affect the hydrodynamics of estuarine systems. This study provides a holistic view of the longitudinal nature and character of sediment in an urban estuary, the Galveston Bay Estuary System (GBES), under daily and extreme flow regimes and presents the results of water and sediment sampling after Hurricane Harvey. The sediment sampling quantified total suspended sediment (TSS) concentrations, metal concentrations, and the diversity of microbial communities. The results revealed the impact of the substantial sediment loads that were transported into the GBES in terms of sediment grain type, the spatial distribution of trace metals, and the diversity of microbial communities. A measurable shift in the percentage of silt relative to historical norms was noted in the GBES after Hurricane Harvey. Not only did sediment metal data confirms this shift and its ensuing impact on metal concentrations; microbial data provided ample evidence of the effect of leaks and spills from wastewater treatment plants, superfund sites, and industrial runoff on microbial diversity. The research demonstrates the importance of understanding longitudinal sediment transport and deposition in estuarine systems under daily flow regimes but more critically, following natural hazard events to ensure sustainability and resilience of systems such as the GBES that encounter numerous acute and chronic stresses.

Depth-structuring of multi-kingdom soil communities in agricultural pastures

The biodiversity and structure of deep agricultural soil communities are poorly understood, especially for eukaryotes. Using DNA metabarcoding and co-occurrence networks, we tested whether prokaryote, fungal, protist, and nematode biodiversity declines with increasing depth (0-0.1,  0.3-0.5,  and 1.1-1.7m) in pastoral soil; whether deep soil organisms are subsets of those at the surface; and whether multi-kingdom networks become more interconnected with increasing depth. Depth-related richness declines were observed for almost all detected fungal classes, protist phyla, and nematode orders, but only 13 of 25 prokaryote phyla, of which nine had increasing richness with depth. Deep soil communities were not simply subsets of surface communities, with 3.8%-12.2% of eukaryotes and 13.2% of prokaryotes detected only in the deepest samples. Eukaryotes mainly occurred in the upper soil layers whereas prokaryotes were more evenly distributed across depths. Plant-feeding nematodes were most abundant in top soil, whereas bacteria feeders were more abundant in deep soil. Co-occurrence network structure differences suggested that deep soil communities are concentrated around scarce niches of resource availability, in contrast to more spatially homogenous and abundant resources at the surface. Together, these results demonstrate effects of depth on the composition, distribution, and structure of prokaryote and eukaryote soil communities.

Microbial diversity in tropical marine sediments assessed using culture-dependent and culture-independent techniques

The microbial communities associated with marine sediments are critical for ecosystem function yet remain poorly characterized. While culture-independent (CI) techniques capture the broadest perspective on community composition, culture-dependent (CD) methods can select for low abundance taxa that are missed using CI approaches. This study aimed to assess microbial diversity in tropical marine sediments at five shallow-water sites in Belize using both CD and CI techniques. The CD methods captured approximately 3% of the >800 genera detected across all sites using the CI approach. Additionally, 39 genera were only detected in culture, revealing rare taxa that were missed with the CI approach. Significantly different communities were detected across sites, with rare taxa playing an important role in distinguishing among communities. This study provides important baseline data describing shallow-water sediment microbial communities, evidence that standard cultivation techniques may be more effective than previously recognized, and the first steps towards identifying new taxa that are amenable to agar plate cultivation.

Profiling of Microbial Communities in the Sediments of Jinsha River Watershed Exposed to Different Levels of Impacts by the Vanadium Industry, Panzhihua, China

The mining, smelting, manufacturing, and disposal of vanadium (V) and associated products have caused serious environmental problems. Although the microbial ecology in V-contaminated soils has been intensively studied, the impacted watershed ecosystems have not been systematically investigated. In this study, geochemistry and microbial structure were analyzed along ~30 km of the Jinsha River and its two tributaries across the industrial areas in Panzhihua, one of the primary V mining and production cities in China. Geochemical analyses showed different levels of contamination by metals and metalloids in the sediments, with high degrees of contamination observed in one of the tributaries close to the industrial park. Analyses of the V4 hypervariable region of 16S rRNA genes of the microbial communities in the sediments showed significant decrease in microbial diversity and microbial structure in response to the environmental gradient (e.g., heavy metals, total sulfur, and total nitrogen). Strong association of the taxa (e.g., Thauera, Algoriphagus, Denitromonas, and Fontibacter species) with the metals suggested selection for these potential metal-resistant and/or metabolizing populations. Further co-occurrence network analysis showed that many identified potential metal-mediating species were among the keystone taxa that were closely associated in the same module, suggesting their strong inter-species interactions but relative independence from other microorganisms in the hydrodynamic ecosystems. This study provided new insight into the microbe-environment interactions in watershed ecosystems differently impacted by the V industries. Some of the phylotypes identified in the highly contaminated samples exhibited potential for bioremediation of toxic metals (e.g., V and Cr).

Ecological risk potentials of petroleum hydrocarbons and heavy metals shape the bacterial communities of marine hydrosphere at Atlantic Ocean, Atlas Cove, Nigeria

Trans-Atlantic voyage of petroleum often leads to marine pollution with petroleum hydrocarbons (PHs) and heavy metals (HMs) that defines structures of autochthonous bacteria in the hydrosphere. Bacterial taxa of marine sediments exposed to petroleum transport activities were profiled using 16S rDNA metagenomics and correlated with the geochemistry to establish their impact on the microbiome. The physico-chemistry of the marine systems revealed varied degrees of contamination with PHs and HMs exceeding recommended threshold for aquatic life. Ecological risk assessment based on organic carbon of the sediment established phenanthrene, anthracene, and pyrene posed high risks (index risk quotient >32) to marine life. The most dominant phylum of the 44 bacterial phyla in the marine-sphere was Proteobacteria with relative abundance of 45-77% in the sampling locations. Relative dominance of Proteobacteria in the sediments spanned Gammaproteobacteria (17-25%), Deltaproteobacteria (12-20%), and Alphaproteobacteria (7-14%). Whereas, more operational taxonomic units (OTUs) belonging to Epsilonproteobacteria (19 ± 2.4%) were found in estuarine sediment unlike < 0.5% relative abundances obtained from oceanic sediments. Sulfurimonas apparently dominated the bacterial genera with up to 2.16 ± 0.19% abundance in oceanic sediments. Canonical correspondence analysis revealed that PHs shaped the structure of bacterial OTUs in oceanic sediments where petroleum loading/offloading occurs unlike in some kilometres a yonder where HMs correlated with the bacteria structure. The dominant bacteria might possibly pivotal to ecophysiologies of hydrocarbon contaminated marine environment, and would be pertinent to biotechnological applications for possible bioremediation campaign.

Comparing Sediment Microbiomes in Contaminated and Pristine Wetlands along the Coast of Yucatan

Microbial communities are important players in coastal sediments for the functioning of the ecosystem and the regulation of biogeochemical cycles. They also have great potential as indicators of environmental perturbations. To assess how microbial communities can change their composition and abundance along coastal areas, we analyzed the composition of the microbiome of four locations of the Yucatan Peninsula using 16S rRNA gene amplicon sequencing. To this end, sediment from two conserved (El Palmar and Bocas de Dzilam) and two contaminated locations (Sisal and Progreso) from the coast northwest of the Yucatan Peninsula in three different years, 2017, 2018 and 2019, were sampled and sequenced. Microbial communities were found to be significantly different between the locations. The most noticeable difference was the greater relative abundance of Planctomycetes present at the conserved locations, versus FBP group found with greater abundance in contaminated locations. In addition to the difference in taxonomic groups composition, there is a variation in evenness, which results in the samples of Bocas de Dzilam and Progreso being grouped separately from those obtained in El Palmar and Sisal. We also carry out the functional prediction of the metabolic capacities of the microbial communities analyzed, identifying differences in their functional profiles. Our results indicate that landscape of the coastal microbiome of Yucatan sediment shows changes along the coastline, reflecting the constant dynamics of coastal environments and their impact on microbial diversity.

Integrating pan-genome with metagenome for microbial community profiling

Advances in sequencing technology have led to the increased availability of genomes and metagenomes, which has greatly facilitated microbial pan-genome and metagenome analysis in the community. In line with this trend, studies on microbial genomes and phenotypes have gradually shifted from individuals to environmental communities.

Pan-genomics and metagenomics are powerful strategies for in-depth profiling study of microbial communities. Pan-genomics focuses on genetic diversity, dynamics, and phylogeny at the multi-genome level, while metagenomics profiles the distribution and function of culture-free microbial communities in special environments. Combining pan-genome and metagenome analysis can reveal the microbial complicated connections from an individual complete genome to a mixture of genomes, thereby extending the catalog of traditional individual genomic profile to community microbial profile. Therefore, the combination of pan-genome and metagenome approaches has become a promising method to track the sources of various microbes and decipher the population-level evolution and ecosystem functions.

This review summarized the pan-genome and metagenome approaches, the combined strategies of pan-genome and metagenome, and applications of these combined strategies in studies of microbial dynamics, evolution, and function in communities. We discussed emerging strategies for the study of microbial communities that integrate information in both pan-genome and metagenome. We emphasized studies in which the integrating pan-genome with metagenome approach improved the understanding of models of microbial community profiles, both structural and functional. Finally, we illustrated future perspectives of microbial community profile: more advanced analytical techniques, including big-data based artificial intelligence, will lead to an even better understanding of the patterns of microbial communities.

Contrasting community assembly processes structure lotic bacteria metacommunities along the river continuum

The heterogeneous nature of lotic habitats plays an important role in the complex ecological and evolutionary processes that structure the microbial communities within them. Due to such complexity, our understanding of lotic microbial ecology still lacks conceptual frameworks for the ecological processes that shape these communities. We explored how bacterial community composition and underlying ecological assembly processes differ between lotic habitats by examining community composition and inferring community assembly processes across four major habitat types (free-living, particle-associated, biofilm on benthic stones and rocks, and sediment). This was conducted at 12 river sites from headwater streams to the main river in the River Thames, UK. Our results indicate that there are distinct differences in the bacterial communities between four major habitat types, with contrasting ecological processes shaping their community assembly processes. While the mobile free-living and particle-associated communities were consistently less diverse than the fixed sediment and biofilm communities, the latter two communities displayed higher homogeneity across the sampling sites. This indicates that the relative influence of deterministic environmental filtering is elevated in sediment and biofilm communities compared with free-living and particle-associated communities, where stochastic processes play a larger role.

Long-term agricultural contamination shaped diversity response of sediment microbiome

The pollution caused by agricultural production poses a threat to the ecological integrity of river ecosystems, altering the structure and function of river ecosystems. Differences in microbial community structure provide useful information about the impact of agricultural pollution on the biological integrity of ecosystems, but generally convey little information regarding ecosystem functions. In this study, using Illumina MiSeq sequencing technology based on the 16S rRNA gene, river sediment samples associated with four different types of agricultural pollution were comprehensively analyzed. The results show that the total organic carbon (TOC) content was highest at the YZS site (animal husbandry sewage) among the assayed sites, but the species richness and uniformity were lowest at this site, which may have been caused by the high nutrient source of the sewage. Furthermore, in the three YZS samples affected by the long-term discharge of aquaculture tail-water, the unique genus Dechloromonas and the genus Candidatus-Competitor were observed, which are strongly correlated with phosphorus conversion. The formation of network modules may correspond to the coexistence of functional bacteria accustomed to multiple niche combinations under different agricultural pollution conditions in river sediments. According to the PICRUSt functional prediction, the bacterial community in the agricultural polluted river sediment primarily harbored 46 subfunctions, exhibiting richness of functions. Overall, our results provide a more comprehensive understanding of the structure and ecological processes associated with the aggregation of bacterial communities, which is beneficial for the management of river environments.

Prokaryotic and microeukaryotic communities in an experimental rice plantation under long-term use of pesticides

Conventional agricultural practices, such as rice plantations, often contaminate the soil and water with xenobiotics. Here we evaluated the microbiota composition in experimental rice planting with a record of prolonged pesticide use, using 16S and 18S rRNA amplicon sequencing. We investigated four components of a complete agricultural system: affluent water (A), rice rhizosphere soil (R), sediment from a storage pond (S), and effluent (E) water (drained from the storage pond). Despite the short spatial distance between our sites, the beta diversity analysis of bacterial communities showed two well-defined clusters, separating the water and sediment/rhizosphere samples; rhizosphere and sediment were richer while the effluent was less diverse. Overall, the site with the highest evenness was the rhizosphere. Unlike the bacterial communities, Shannon diversity of microeukaryotes was significantly different between A and E. The effluent presented the lowest values for all ecological indexes tested and differed significantly from all sampled sites, except on evenness. When mapped the metabolic pathways, genes corresponding to the degradation of aromatic compounds, including genes related to pesticide degradation, were identified. The most abundant genes were related to the degradation of benzoate. Our results indicate that the effluent is a selective environment for fungi. Interestingly, the overall fungal diversity was higher in the affluent, the water that reached the system before pesticide application, and where the prokaryotic diversity was the lowest. The affluent and effluent seem to have the lowest environmental quality, given the presence of bacteria genera previously recorded in environments with high concentrations of pesticide residues. The microbiota, environmental characteristics, and pesticide residues should be further studied and try to elucidate the potential for pesticide degradation by natural consortia. Thus, extensive comparative studies are needed to clarify the microbial composition, diversity, and functioning of rice cultivation environments, and how pesticide use changes may reflect differences in microbial structure.

Seagrass vegetation affect the vertical organization of microbial communities in sediment

Seagrasses represent high primary productivity and provide important ecosystem services to the marine environment. Seagrass-associated microbial communities are playing essential ecological functional roles in biogeochemical cycles. However, little is known about the effect of seagrass vegetation on microbial communities in sediment. In the present study, the sediment cores of seagrass bed (dominated by Zostera japonica and Zostera marine) and degradation area in Swan Lake (China) were sampled; then, biogeochemical parameters were analyzed, and microbial community composition was investigated by using high-throughput sequencing of the 16S rRNA gene. The results showed that the presence of seagrass could lead to a decrease in the richness and diversity of the microbial community. In the vertical direction, a pronounced shift from Proteobacteria-dominated upper layers to Chloroflexi and Crenarchaeota-dominated deep layers in all sediment cores were observed. Besides, Bathyarchaeia is more abundant at degradation area, while Vibrionaceae, Sulfurovum and Lokiarchaeial overrepresent at the seagrass bed area. Vibrionaceae was abundant in the rhizosphere of Z. marina and Z. japonica, and the proportions reached 84.45% and 63.89%, respectively. This enrichment of Vibrio spp. may be caused by the macrobenthic species near the seagrass rhizosphere, and these Vibrio spp. reduced the diversity and stability of microbial community, which may lead to the degradation of seagrass. This study would provide clues for the distribution patterns and niche preferences of seagrass microbiome. The conservation strategy of seagrass would be further elucidated from the perspective of the microbiome.

The responses of soil enzyme activities, microbial biomass and microbial community structure to nine years of varied zinc application rates

Zinc (Zn) fertilizer application can certainly improve the production and nutritional quality of cereal crops. However, Zn accumulation in the soil may lead to some deleterious environmental impacts in agroecosystems. The effects of long-term Zn application on soil microbial properties remain unclear, but it is imperative to understand such effects. In this study, we collected soil samples from a nine-year field experiment in a wheat-maize system that continuously received Zn applied at various rates (0, 2.3, 5.7, 11.4, 22.7 and 34.1 kg ha^-1) to evaluate the soil enzymes, microbial biomass and microbial community structure. The results showed that Zn application at the rate of 5.7 kg ha^-1 significantly increased the activities of urease, invertase, alkaline phosphatase and catalase in the soil, while the rate of 34.1 kg ha^-1 significantly decreased the evaluated enzyme activities. The microbial biomass carbon (C) and nitrogen (N) were not affected by Zn application rates, although an increase in the microbial biomass C was observed in the 11.4 kg ha^-1 treatment. Moreover, the alpha diversity of the bacterial and fungal communities did not vary among the nil Zn, optimal Zn (5.7 kg ha^-1) and excess Zn (34.1 kg ha^-1) treatments. However, the bacterial communities in the soil receiving the optimal and excess Zn application rates were slightly changed. Compared to the nil Zn treatment, the other Zn application rates increased the relative abundances of the Rhodospirillales, Gaiellales and Frankiales orders and decreased the abundance of the Latescibacteria phylum. The redundancy analysis further indicated that the soil bacterial community composition significantly correlated with the concentrations of soil DTPA-Zn and total Zn. These results highlight the importance of optimal Zn application in achieving high production and high grain quality while concurrently promoting soil microbial activity, improving the bacterial community and further maintaining the sustainability of the agroecological environment.

Source identification of phosphorus in the river-lake interconnected system using microbial community fingerprints

Phosphorus, one of the primary limiting factors for eutrophication, plays a crucial role in the ecology health of aquatic ecosystems. However, understanding phosphorus bioavailability and source contributions in contaminated lake sediments which could help develop effective eutrophication management plans is limited largely due to the lack of appropriate methods in large catchments with a complex arrangement of sources. Based on the significant relationships between sediment, phosphorus and microbial community, source-specific microbial community fingerprints formed by machine-learning classification SourceTracker might shed light on determining dominant phosphorus sources in the river-lake systems in the era of high-throughput sequencing. This study was conducted in Dongting Lake that suffered accelerated eutrophication due to considerable phosphorus input from the inflow-rivers. The results of phosphorus fractionation according to the Standards, Measurements and Testing harmonized procedure indicated that sediments in the central lake had a higher concentration of non-apatite inorganic phosphorus (Mann-Whitney U test), which deserves greater attention on the risk of phosphorus release. The significant relationships between phosphorus fractionations, sediment and bacterial community were established with the spearman correlation and network analysis. SourceTracker analysis indicated that the major inflow-rivers of phosphorus sources to Dongting Lake were the Songzi, Miluo, and Xinqiang Rivers. The effects of sediment diffusion distance on phosphorus source apportionment were further confirmed. Taken together, our results contribute to an improved understanding of phosphorus fractionations and source contributions in the river-lake systems and its potential impact to eutrophication management plans.

Earth microbial co-occurrence network reveals interconnection pattern across microbiomes

BACKGROUND

Microbial interactions shape the structure and function of microbial communities; microbial co-occurrence networks in specific environments have been widely developed to explore these complex systems, but their interconnection pattern across microbiomes in various environments at the global scale remains unexplored. Here, we have inferred an Earth microbial co-occurrence network from a communal catalog with 23,595 samples and 12,646 exact sequence variants from 14 environments in the Earth Microbiome Project dataset.

RESULTS

This non-random scale-free Earth microbial co-occurrence network consisted of 8 taxonomy distinct modules linked with different environments, which featured environment specific microbial co-occurrence relationships. Different topological features of subnetworks inferred from datasets trimmed into uniform size indicate distinct co-occurrence patterns in the microbiomes of various environments. The high number of specialist edges highlights that environmental specific co-occurrence relationships are essential features across microbiomes. The microbiomes of various environments were clustered into two groups, which were mainly bridged by the microbiomes of plant and animal surface. Acidobacteria Gp2 and Nisaea were identified as hubs in most of subnetworks. Negative edges proportions ranged from 1.9% in the soil subnetwork to 48.9% the non-saline surface subnetwork, suggesting various environments experience distinct intensities of competition or niche differentiation. Video abstract CONCLUSION: This investigation highlights the interconnection patterns across microbiomes in various environments and emphasizes the importance of understanding co-occurrence feature of microbiomes from a network perspective.

Phylum-level diversity of the microbiome of the extremophilic basidiomycete fungus Pisolithus arhizus (Scop.) Rauschert: An island of biodiversity in a thermal soil desert

We used high‐throughput DNA sequencing methods combined with bio‐geochemical profiles to characterize the internal environment and community structure of the microbiome of the basidiomycete fungus Pisolithus arhizus (Scop.) Rauschert from soils within a geothermal feature of Yellowstone National Park. Pisolithus arhizus is unique in that it forms closed fruiting bodies that sequester visible sulfur within. Fourier transform infrared spectroscopy (FTIR) analysis demonstrates that the P. arhizus fruiting body also concentrates copper, manganese, nickel, and zinc and contains pure granular silica. Gas chromatography‐mass spectrometry (GC‐MS) analysis indicates an environment rich in hydrocarbons. Oxygen probe analysis reveals that zones of up to 4× atmospheric oxygen exist within nanometers of zones of near anoxia. Analysis of microbial community structure using high‐throughput DNA sequencing methods shows that the fruiting body supports a microbiome that reflects the physiochemical environment of the fruiting body. Diversity and richness measures indicate a microbiome that is significantly richer and more diverse than that of the soils in which P. arhizus grows. Further, P. arhizus sporocarps are enriched significantly in Proteobacteria (primarily Burkholderia) Gemmatimonadetes, Bacteroidetes, Verrucomicrobia, Nitrospirae, Elusimicrobia, and Latescibacteria (WS3) while soils are enriched in Actinobacteria (primarily Mycobacterium), Dormibacteraeota (AD3), and Eremiobacteraeota (WPS‐2). Finally, pairwise % similarity comparisons indicate that P. arhizus harbors two lineages that may represent new groups in the candidate phylum radiation (CPR). Together, these results demonstrate that P. arhizus provides a novel environment for microbiome studies and provides for interesting hypotheses regarding the evolution, origins, and functions of symbioses and novel microbes.

Long-term effects of straw return and straw-derived biochar amendment on bacterial communities in soil aggregates

Improving soil structure, fertility, and production is of major concern for establishing sustainable agroecosystems. Further research is needed to evaluate whether different methods of straw returning determine the variations of soil aggregation and the microbial community in aggregates in the long term. In this study, we comparatively investigated the effects of long-term fertilization regimes performed over six years, namely, non-fertilization (CK), chemical fertilization (CF), continuous straw return (CS), and continuous straw-derived biochar amendment (CB), on soil aggregation and bacterial communities in rice-wheat rotation systems. The results showed that straw/biochar application increased soil nutrient content and soil aggregate size distribution and stability at both 0–20 cm and 20–40 cm soil depths, compared with those of CF and CK; CB performed better than CS. CB increased bacterial community diversity and richness in 0–20 cm soil, and evenness in 0–40 cm soil (p < 0.05); CS had no significant effect on these aspects. Variations in the relative abundance of Actinobacteria, Chloroflexi, Bacteroidetes, Nitrospirae, Gemmatimonadetes, and Latescibacteria in specific aggregates confirmed the different effects of straw/biochar on bacterial community structure. The partial least squares discrimination analysis and permutation multivariate analysis of variance revealed that fertilization, aggregate size fractions, and soil depth affected the bacterial community, although their effects differed. This study suggests that CB may reduce chemical fertilizer usage and improve the sustainability of rice-wheat cropping systems over the long term, with a better overall outcome than CS.

Soil Water Contents Control the Responses of Dissolved Nitrogen Pools and Bacterial Communities to Freeze-Thaw in Temperate Soils

Background

Freeze-thaw influences soil-dissolved nitrogen (N) pools due to variations in bacterial communities in temperate regions. The availability of soil water is important to soil biogeochemical cycles under frozen conditions. However, it is unclear how soil water content (SWC) mediates the effects of freeze-thaw on soil-dissolved N pools and bacterial communities.

Method

In this study, freeze-thaw microcosms were incubated at three levels of SWC, including 10% (air-dried soils), 15% (natural SWC), and 30% (wet soils). In addition to measuring soil-dissolved N pools, variations in bacterial communities were examined using high-throughput sequencing. Results and Conclusions. Total dissolved N (TDN), NO₃ ^--N, NH₄ ⁺-N, microbial biomass N (MBN), and net N mineralization rate (NNMR) were significantly influenced by SWC, freeze-thaw, and their interaction (NH₄ ⁺-N excluded). N immobilization was inhibited under both low and high SWC, which was accompanied by varied bacterial community composition. However, only higher SWC substantially modified the freeze-thaw effects on the soil-dissolved N pools, characterized by a decrease in N mineralization (especially for the content of NO₃ ^--N and NNMR) and an increase in N immobilization (MBN). These scenarios could be significantly correlated to variations in bacterial community composition based on redundancy analysis, especially by species belonging to Bacteroidetes, Nitrospirae, Alphaproteobacteria, Gemmatimonadetes, and Verrucomicrobia (Spearman's correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.Bacteroidetes, Nitrospirae, Alphaproteobacteria, Gemmatimonadetes, and Verrucomicrobia (Spearman's correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.Nitrospirae, Alphaproteobacteria, Gemmatimonadetes, and Verrucomicrobia (Spearman's correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.Alphaproteobacteria, Gemmatimonadetes, and Verrucomicrobia (Spearman's correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.Gemmatimonadetes, and Verrucomicrobia (Spearman's correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.Verrucomicrobia (Spearman's correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.

Hiding in Plain Sight: The Globally Distributed Bacterial Candidate Phylum PAUC34f

Bacterial candidate phylum PAUC34f was originally discovered in marine sponges and is widely considered to be composed of sponge symbionts. Here, we report 21 single amplified genomes (SAGs) of PAUC34f from a variety of environments, including the dark ocean, lake sediments, and a terrestrial aquifer. The diverse origins of the SAGs and the results of metagenome fragment recruitment suggest that some PAUC34f lineages represent relatively abundant, free-living cells in environments other than sponge microbiomes, including the deep ocean. Both phylogenetic and biogeographic patterns, as well as genome content analyses suggest that PAUC34f associations with hosts evolved independently multiple times, while free-living lineages of PAUC34f are distinct and relatively abundant in a wide range of environments.

Metabolic potentials of archaeal lineages resolved from metagenomes of deep Costa Rica sediments

Numerous archaeal lineages are known to inhabit marine subsurface sediments, although their distributions, metabolic capacities, and interspecies interactions are still not well understood. Abundant and diverse archaea were recently reported in Costa Rica (CR) margin subseafloor sediments recovered during IODP Expedition 334. Here, we recover metagenome-assembled genomes (MAGs) of archaea from the CR margin and compare them to their relatives from shallower settings. We describe 31 MAGs of six different archaeal lineages (Lokiarchaeota, Thorarchaeota, Heimdallarchaeota, Bathyarcheota, Thermoplasmatales, and Hadesarchaea) and thoroughly analyze representative MAGs from the phyla Lokiarchaeota and Bathyarchaeota. Our analysis suggests the potential capability of Lokiarchaeota members to anaerobically degrade aliphatic and aromatic hydrocarbons. We show it is genetically possible and energetically feasible for Lokiarchaeota to degrade benzoate if they associate with organisms using nitrate, nitrite, and sulfite as electron acceptors, which suggests a possibility of syntrophic relationships between Lokiarchaeota and nitrite and sulfite reducing bacteria. The novel Bathyarchaeota lineage possesses an incomplete methanogenesis pathway lacking the methyl coenzyme M reductase complex and encodes a noncanonical acetogenic pathway potentially coupling methylotrophy to acetogenesis via the methyl branch of Wood-Ljungdahl pathway. These metabolic characteristics suggest the potential of this Bathyarchaeota lineage to be a transition between methanogenic and acetogenic Bathyarchaeota lineages. This work expands our knowledge about the metabolic functional repertoire of marine benthic archaea.

Strong Seasonality in Arctic Estuarine Microbial Food Webs

Microbial communities in the coastal Arctic Ocean experience extreme variability in organic matter and inorganic nutrients driven by seasonal shifts in sea ice extent and freshwater inputs. Lagoons border more than half of the Beaufort Sea coast and provide important habitats for migratory fish and seabirds; yet, little is known about the planktonic food webs supporting these higher trophic levels. To investigate seasonal changes in bacterial and protistan planktonic communities, amplicon sequences of 16S and 18S rRNA genes were generated from samples collected during periods of ice-cover (April), ice break-up (June), and open water (August) from shallow lagoons along the eastern Alaska Beaufort Sea coast from 2011 through 2013. Protist communities shifted from heterotrophic to photosynthetic taxa (mainly diatoms) during the winter–spring transition, and then back to a heterotroph-dominated summer community that included dinoflagellates and mixotrophic picophytoplankton such as Micromonas and Bathycoccus. Planktonic parasites belonging to Syndiniales were abundant under ice in winter at a time when allochthonous carbon inputs were low. Bacterial communities shifted from coastal marine taxa (Oceanospirillaceae, Alteromonadales) to estuarine taxa (Polaromonas, Bacteroidetes) during the winter-spring transition, and then to oligotrophic marine taxa (SAR86, SAR92) in summer. Chemolithoautotrophic taxa were abundant under ice, including iron-oxidizing Zetaproteobacteria. These results suggest that wintertime Arctic bacterial communities capitalize on the unique biogeochemical gradients that develop below ice near shore, potentially using chemoautotrophic metabolisms at a time when carbon inputs to the system are low. Co-occurrence networks constructed for each season showed that under-ice networks were dominated by relationships between parasitic protists and other microbial taxa, while spring networks were by far the largest and dominated by bacteria-bacteria co-occurrences. Summer networks were the smallest and least connected, suggesting a more detritus-based food web less reliant on interactions among microbial taxa. Eukaryotic and bacterial community compositions were significantly related to trends in concentrations of stable isotopes of particulate organic carbon and nitrogen, among other physiochemical variables such as dissolved oxygen, salinity, and temperature. This suggests the importance of sea ice cover and terrestrial carbon subsidies in contributing to seasonal trends in microbial communities in the coastal Beaufort Sea.

Sediment bacterial communities associated with environmental factors in Intermittently Closed and Open Lakes and Lagoons (ICOLLs)

Intermittently Closed and Open Lakes and Lagoons (ICOLLS) are important coastal systems that are periodically separated from the ocean by a sand barrier or a berm. In urban ICOLLs, continuous inputs of organic material and nutrients into coastal lagoons are contributing to eutrophic conditions that, together with natural environmental factors have implications for the resident sediment bacterial communities. We used molecular tools to investigate the ecological communities of four ICOLLs; Narrabeen, Dee Why, Curl Curl and Manly in Sydney, Australia, which have been subjected to increasing pressure from anthropogenic activities over the last century. We used targeted gene sequencing of the prokaryotic 16S ribosomal RNA gene to describe the bacterial diversity and community structure and discuss differences with respect to environmental factors at the ICOLL scale (e.g. size, shape, normalised N loading) and site scale (e.g. water and sediment quality) within each lagoon. Due to differences in hydrological patterns, we expected that sediment bacterial communities would be more heterogenous in displacement-dominated lagoons (Curl Curl and Manly) than the mixing-dominated lagoons (Narrabeen and Dee Why). Interestingly, we did not find strong relationships between the main bacterial groups and distance from the lagoon entrance (used as a proxy for salinity and silt) in the displacement-dominated lagoons. Moreover, we found that α diversity was highest in Narrabeen and Manly lagoons despite differences in lagoon size and shape. Furthermore, while bacterial community structure was similar in Curl Curl and Dee Why, communities in Manly and Narrabeen differed along temperature/TOC and salinity/silt gradients respectively. In Manly lagoon, we found relatively more anaerobic bacteria such as Epsilonbactereota which is involved in the oxidation and reduction of sulfur compounds. Moreover, we identified several bacterial taxa (including sulfur metabolising Chlorobiaceae) related to increasing TOC that could be investigated further as potential indicators of excess enrichment.

Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader 'Candidatus Leucobacter sulfamidivorax' strain GP

Background

Microbial communities recurrently establish metabolic associations resulting in increased fitness and ability to perform complex tasks, such as xenobiotic degradation. In a previous study, we have described a sulfonamide-degrading consortium consisting of a novel low-abundant actinobacterium, named strain GP, and Achromobacter denitrificans PR1. However, we found that strain GP was unable to grow independently and could not be further purified.

Results

Previous studies suggested that strain GP might represent a new putative species within the Leucobacter genus (16S rRNA gene similarity < 97%). In this study, we found that average nucleotide identity (ANI) with other Leucobacter spp. ranged between 76.8 and 82.1%, further corroborating the affiliation of strain GP to a new provisional species. The average amino acid identity (AAI) and percentage of conserved genes (POCP) values were near the lower edge of the genus delimitation thresholds (65 and 55%, respectively). Phylogenetic analysis of core genes between strain GP and Leucobacter spp. corroborated these findings. Comparative genomic analysis indicates that strain GP may have lost genes related to tetrapyrrole biosynthesis and thiol transporters, both crucial for the correct assembly of cytochromes and aerobic growth. However, supplying exogenous heme and catalase was insufficient to abolish the dependent phenotype. The actinobacterium harbors at least two copies of a novel genetic element containing a sulfonamide monooxygenase (sadA) flanked by a single IS1380 family transposase. Additionally, two homologs of sadB (4-aminophenol monooxygenase) were identified in the metagenome-assembled draft genome of strain GP, but these were not located in the vicinity of sadA nor of mobile or integrative elements.

Conclusions

Comparative genomics of the genus Leucobacter suggested the absence of some genes encoding for important metabolic traits in strain GP. Nevertheless, although media and culture conditions were tailored to supply its potential metabolic needs, these conditions were insufficient to isolate the PR1-dependent actinobacterium further. This study gives important insights regarding strain GP metabolism; however, gene expression and functional studies are necessary to characterize and further isolate strain GP. Based on our data, we propose to classify strain GP in a provisional new species within the genus Leucobacter, ‘Candidatus Leucobacter sulfamidivorax‘.

A Preliminary Study of Biliary Microbiota in Patients with Bile Duct Stones or Distal Cholangiocarcinoma

Background and Objective

The distal cholangiocarcinoma (dCCA) is associated with many factors: genes, environment, infection, etc. The current changes in biliary flora are thought to be involved in the formation of many gastrointestinal tract (GIT) diseases, like colon adenocarcinoma. Therefore we want to investigate whether the dCCA has a certain correlation with biliary microecology, and to detect specific strains.

Methods

A total of 68 adults were enrolled, of whom 8 with dCCA, 16 with recurrent choledocholithiasis, and 44 with the onset of common bile duct stones. Endoscopic Retrograde Cholangiopancretography (ERCP) was utilized to collect bile samples for DNA extraction and 16S rRNA gene sequencing, followed by analysis of bile microbiota composition.

Results

First, Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria are the most dominant phyla in the bile of patients with dCCA and the onset of common bile duct stoes. Secondly, compared with the onset of common bile duct stones patients, we got a significant increase in the phylum Gemmatimonadetes, Nitrospirae, Chloroflexi, Latescibacteria, and Planctomycetes in dCCA patients. Finally, at the genus level, we obtained sequencing results of 252 bacterial genera from patients with dCCA, recurrent choledocholithiasis, and the new onset of common bile duct stones, revealing heterogeneity among individuals.

Conclusion

To the best of our knowledge, this is the first study of the dysbiosis of bile flora in patients with dCCA. This micro-ecological disorder may be a decisive factor in the formation of dCCA. At the same time, for the first time, this study provides a test chart of biliary microbial populations that may be associated with recurrent choledocholithiasis. The compositional changes of the core microbial group of the biliary tract have potentially important biological and medical significance for the microbiological biliary disorders of dCCA.

The Wood-Ljungdahl pathway as a key component of metabolic versatility in candidate phylum Bipolaricaulota (Acetothermia, OP1)

The Wood-Ljungdahl (WL) pathway is an important component of the metabolic machinery in multiple anaerobic prokaryotes, including numerous yet-uncultured bacterial phyla. The pathway can operate in the reductive and oxidative directions, enabling a wide range of metabolic processes. Here, we present a detailed analysis of 14 newly acquired, previously analysed, and publicly available genomic assemblies belonging to the candidate phylum Bipolaricaulota (candidate division OP1, and candidatus Acetothermia), where the occurrence of WL pathway appears to be universal. In silico analysis of predicted metabolic capabilities indicates that the pathway enables homoacetogenic fermentation of sugars and amino acids in all three Bipolaricaulota orders (RBG-16-55-9, UBA7950 and Bipolaricaulales). In addition, members of RBG-16-55-9 appear to possess the additional capacity for syntrophic acetate oxidation using the WL pathway; as well as for respiratory growth using oxygen or nitrate. Anabolically, all UBA7950, and the majority of the Bipolaricaulales genomes possess the capacity for autotrophic growth using the WL pathway. Our results highlight the WL-enabled metabolic versatility in the Bipolaricaulota, emphasize the need for examining the WL pathway in context of the overall metabolic circuitry in uncultured taxa, and demonstrate the value of comparative genomic analysis for providing a detailed overview of metabolic potential in a target microbial lineage and its potential functional niche in an ecosystem.