Distribution Of Functional Genes Research Articles

Metagenomics profiling of the microbial community and functional differences in solid-state fermentation vinegar starter (seed Pei) from different Chinese regions.

The starter used in solid-state fermentation (SSF) vinegar, known as seed Pei is a microbial inoculant from the previous batch that is utilized during the acetic acid fermentation stage. The seed Pei, which has a notable impact on vinegar fermentation and flavor, is under-researched with comparative studies on microorganisms. Herein metagenomics was employed to reveal the microbes and their potential metabolic functions of four seed Pei from three regions in China. The predominant microbial taxa in all four starters were bacteria, followed by viruses, eukaryotes, and archaea, with Lactobacillus sp. or Acetobacter sp. as main functional taxa. The seed Pei used in Shanxi aged vinegar (SAV) and Sichuan bran vinegar (SBV) exhibited a higher similarity in microbial composition and distribution of functional genes, while those used in two Zhenjiang aromatic vinegar (ZAV) differed significantly. Redundancy analysis (RDA) of physicochemical factors and microbial communities indicated that moisture content, pH, and reducing sugar content are significant factors influencing microbial distribution. Moreover, seven metagenome-assembled genomes (MAGs) that could potentially represent novel species were identified. There are distinctions in the microbiome and functional genes among different seed Pei. The vinegar starters were rich in genes related to carbohydrate metabolism. This research provides a new perspective on formulating vinegar fermentation starters and developing commercial fermentation agents for vinegar production.

Complete sequence of carbapenem-resistant Ralstonia mannitolilytica clinical isolate co-producing novel class D β-lactamase OXA-1176 and OXA-1177 in Japan.

In 2020, the Ralstonia mannitolilytica strain JARB-RN-0044 was isolated from a midstream urine sample of an elderly hospitalized patient in Japan and was highly resistant to carbapenem (i.e., imipenem, meropenem, and doripenem). Whole-genome sequencing revealed that the complete genome consists of two replicons, a 3.5-Mb chromosome and a 1.5-Mb large non-chromosomal replicon which has not been reported in R. mannitolilytica, and referred to as the "megaplasmid" in this study based on Cluster of Orthologous Group of proteins functional analysis. The strain JARB-RN-0044 harbored two novel OXA-60 and OXA-22 family class D β-lactamase genes blaOXA-1176 and blaOXA-1177 on the megaplasmid. Cloning experiments indicated that Escherichia coli recombinant clone expressing blaOXA-1176 gene showed increased minimum inhibitory concentrations (MICs) of imipenem, meropenem, and doripenem, indicating that blaOXA-1176 gene encodes carbapenemase. In contrast, E. coli recombinant clone expressing blaOXA-1177 gene showed increased MICs of piperacillin and cefazolin, but not of carbapenem. Interestingly, the 44.6 kb putative prophage region containing genes encoding phage integrase, terminase, head and tail protein was identified in the downstream region of blaOXA-1176 gene, and comparative analysis with some previously reported R. mannitolilytica isolates revealed that the prophage region was unique to strain JARB-RN-0044. The existence of a highly carbapenem-resistant R. mannitolilytica isolate may raise human health concerns in Japan, where the population is rapidly aging.IMPORTANCERalstonia mannitolilytica is an aerobic non-fermenting Gram-negative rod commonly found in aquatic environments and soil. The bacteria can occasionally cause severe hospital-acquired bloodstream infections in immunocompromised patients and it has been recently recognized as an emerging opportunistic human pathogen. Furthermore, some R. mannitolilytica isolates are resistant to various antimicrobial agents, including β-lactams and aminoglycosides, making antimicrobial therapy challenging and clinically problematic. However, clinical awareness of this pathogen is limited. To our knowledge, in Japan, there has been only one report of a carbapenem-resistant R. mannitolilytica clinical isolate from urine by Suzuki et al. in 2015. In this study, whole-genome sequencing analysis revealed the presence and genetic context of novel blaOXA-1176 and blaOXA-1177 genes on the 1.5 Mb megaplasmid from highly carbapenem-resistant R. mannitolilytica isolate and characterized the overall distribution of functional genes in the chromosome and megaplasmid. Our findings highlight the importance of further attention to R. mannitolilytica isolate in clinical settings.

Spatiotemporal successions of N, S, C, Fe, and As cycling genes in groundwater of a wetland ecosystem: Enhanced heterogeneity in wet season

Microorganisms in wetland groundwater play an essential role in driving global biogeochemical cycles. However, largely due to the dynamics of spatiotemporal surface water-groundwater interaction, the spatiotemporal successions of biogeochemical cycling in wetland groundwater remain poorly delineated. Herein, we investigated the seasonal coevolution of hydrogeochemical variables and microbial functional genes involved in nitrogen, carbon, sulfur, iron, and arsenic cycling in groundwater within a typical wetland, located in Poyang Lake Plain, China. During the dry season, the microbial potentials for dissimilatory nitrate reduction to ammonium and ammonification were dominant, whereas the higher potentials for nitrogen fixation, denitrification, methane metabolism, and carbon fixation were identified in the wet season. A likely biogeochemical hotspot was identified in the area located in the low permeable aquifer near the lake, characterized by reducing conditions and elevated levels of Fe2+ (6.65–17.1 mg/L), NH4+ (0.57–3.98 mg/L), total organic carbon (1.02–1.99 mg/L), and functional genes. In contrast to dry season, higher dissimilarities of functional gene distribution were observed in the wet season. Multivariable statistics further indicated that the connection between the functional gene compositions and hydrogeochemical variables becomes less pronounced as the seasons transition from dry to wet. Despite this transition, Fe2+ remained the dominant driving force on gene distribution during both seasons. Gene-based co-occurrence network displayed reduced interconnectivity among coupled C-N-Fe-S cycles from the dry to the wet season, underpinning a less complex and more destabilizing occurrence pattern. The rising groundwater level may have contributed to a reduction in the stability of functional microbial communities, consequently impacting ecological functions. Our findings shed light on microbial-driven seasonal biogeochemical cycling in wetland groundwater.

Bacterial interference competition and environmental filtering reduce the fungal taxonomic and functional contribution to plant residue decomposition in anoxic paddy soils

Plant residue decomposition is central to soil organic matter formation. Fungi, bacteria, and archaea are all well-known agents of residue decomposition. However, their relative taxonomic and functional contributions to plant residue decomposition in anoxic paddy soils are not well understood, and neither are the factors that govern these contributions. Here, a series of microcosms inoculated with two distinct paddy soils and amended with 13C-labeled rice straw was set up. DNA stable-isotope probing (DNA-SIP) based shotgun metagenomic sequencing was performed to reveal the relative contributions of bacteria, archaea, and fungi in rice straw degradation. Furthermore, the possible underlying mechanisms were investigated, focusing on microbial interspecies interference competition. We found that bacteria and archaea collectively accounted for 96.2∼99.5% (in CS anoxic paddy soil) and 81.7∼96.0% (in YT anoxic paddy soil) of the total abundance, while fungi accounted for only 0.5∼3.8% and 4.0∼18.3%, respectively. Phylogenetic distribution of functional genes encoding the carbohydrate-active enzyme (CAZyme) revealed that 87.7% (in CS anoxic paddy soil) and 80.9% (in YT anoxic paddy soil) of these genes were derived from bacteria and archaea, the remainder (12.3% and 19.1%) coming from fungi. The bacteria-fungi antagonism experiment indicated that fungal growth was indeed markedly inhibited by members of the two well-known antimicrobial compounds producing bacterial groups present, the Actinobacteria and the Bacilli. This study indicates that bacterial interference competition and environmental filtering (i.e., low redox/oxygen conditions) may reduce the contribution of fungi to plant residue decomposition in anoxic paddy field environments. These outcomes are important when constructing models to forecast and/or quantitative the microbial contributions to the global carbon dynamics in anoxic paddy soils.

Co-occurrence of toxic metals, bacterial communities and metal resistance genes in coastal sediments from Bohai bay

Sediment heavy metal contamination poses substantial risks to microbial community composition and functional gene distribution. Bohai Bay (BHB), the second-largest bay in the Bohai Sea, is subject to severe anthropogenic pollution. However, to date, there have been no studies conducted to evaluate the distribution of metal resistance genes (MRGs) and bacterial communities in the coastal sediments of BHB. In this study, we employed high-throughput sequencing based on 16S rRNA genes and real-time quantitative PCR (qPCR) to provide a comprehensive view of toxic metals, MRGs, and bacterial communities in BHB's coastal sediment samples across two seasons. We detected high levels of Cd in the summer samples and As in the autumn samples. The metal content in most autumn samples and all summer samples, based on ecological indices, indicated low ecological risk. Proteobacteria dominated all samples, followed by Desulfobacterota, Bacteroidota and Campilobacterota. Bacterial community variability was higher between autumn sampling sites but more stable in summer. We detected 9 MRG subtypes in all samples, with abundances ranging from 4.58 × 10−1 to 2.25 copies/16S rRNA copies. arsB exhibited the highest relative abundance, followed by acr3, czcA and arrA. The efflux mechanism is a common mechanism for sediment resistance to metal stress in Bohai Bay. Procrustes analysis indicated that bacterial community composition may be a determinant of MRGs composition in BHB sediments. Network analysis suggested that eight classes could be potential hosts for six MRGs. However, this type of correlation requires further validation. To summarize, our study offers preliminary insights into bacterial community and MRG distribution patterns in heavy metal-exposed sediments, laying the groundwork for understanding microbial community adaptations in multi-metal polluted environments and supporting ecological restoration efforts.

Metapangenomic investigation provides insight into niche differentiation of methanogenic populations from the subsurface serpentinizing environment, Samail Ophiolite, Oman.

Serpentinization reactions produce highly reduced waters that have hyperalkaline pH and that can have high concentrations of H2 and CH4. Putatively autotrophic methanogenic archaea have been identified in the subsurface waters of the Samail Ophiolite, Sultanate of Oman, though the strategies to overcome hyperalkaline pH and dissolved inorganic carbon limitation remain to be fully understood. Here, we recovered metagenome assembled genomes (MAGs) and applied a metapangenomic approach to three different Methanobacterium populations to assess habitat-specific functional gene distribution. A Type I population was identified in the fluids with neutral pH, while a Type II and "Mixed" population were identified in the most hyperalkaline fluids (pH 11.63). The core genome of all Methanobacterium populations highlighted potential DNA scavenging techniques to overcome phosphate or nitrogen limitation induced by environmental conditions. With particular emphasis on the Mixed and Type II population found in the most hyperalkaline fluids, the accessory genomes unique to each population reflected adaptation mechanisms suggesting lifestyles that minimize niche overlap. In addition to previously reported metabolic capability to utilize formate as an electron donor and generate intracellular CO2, the Type II population possessed genes relevant to defense against antimicrobials and assimilating potential osmoprotectants to provide cellular stability. The accessory genome of the Mixed population was enriched in genes for multiple glycosyltransferases suggesting reduced energetic costs by adhering to mineral surfaces or to other microorganisms, and fostering a non-motile lifestyle. These results highlight the niche differentiation of distinct Methanobacterium populations to circumvent the challenges of serpentinization impacted fluids through coexistence strategies, supporting our ability to understand controls on methanogenic lifestyles and adaptations within the serpentinizing subsurface fluids of the Samail Ophiolite.

Quantitative Responses of Active Ammonia-Oxidizing Archaea and Bacteria to the Biological and Abiotic Factors Across Functional gene Distribution in Coastal Wetlands

Quantitative Responses of Active Ammonia-Oxidizing Archaea and Bacteria to the Biological and Abiotic Factors Across Functional gene Distribution in Coastal Wetlands

Microbial mediated arsenate reducing behavior in landfill leachate-saturated zone

As(V) reduction mediated by microorganisms might be an essential process in resisting As toxicity since As(V) is the major species in the landfill. LSZ has been considered as a trigger of all types of microbial activity inside a landfill site. This research investigated the microbial As(V)-reducing behavior in LSZ. The results revealed that higher As(V)-reduction efficiency in higher As(V) content-stress LSZ scenario. The corresponding microbial diversity also varied with the As(V) content. The microbial community structure was related to arrA and arsC distribution, which encode respiratory As(V) reductase and cytoplasmic As(V) reductase, respectively. The landfill As bio-reduction pathways were modeled, as well as the As functional gene distribution among different As(V) contents at different landfill stages. The C, N, and S metabolic processes generally affected the As(V)-resistance genes distribution. Thiosulfate oxidation, denitrification, and dissimilatory nitrate reduction positively affected arsC, while dissimilatory sulfate reduction and methanogenesis trended to play a negative role. This research provides new insight into As(V) bio-reduction inside a landfill site in terms of functional genes distribution and correlation with nutrient elements metabolic processes.

Linkage between microbial functional genes and net N mineralisation in forest soils along an elevational gradient

AbstractSoil net nitrogen (N) mineralisation, the difference between organic nitrogen mineralisation and mineral nitrogen immobilisation, changes with elevation, thereby determining plant productivity and soil N cycling along elevation gradients. However, it has yet to be established how different microbial functional genes influence the rate of soil net N mineralisation along such gradients. To address this deficiency in our current knowledge, we performed metagenomic sequencing to identify soil microbial functional genes encoding enzymes involved in N cycling at five forest sites along an elevational gradient spanning a range from 1503 to 3182 m above sea level. Our results indicate that the rate of net N mineralisation follows a unimodal pattern with increasing elevation, with a peak (0.18 mg kg−1 d−1) being detected at the mid‐high elevation site. Further, we detected a significant correlation between the abundance of genes encoding enzymes involved in denitrification and ammonia assimilation pathways and net N mineralisation rate (p < 0.05). Moreover, we established that microbial species in the phyla Cyanobacteria, Acidobacteria and Planctomycetes, harbouring keystone functional genes, play a predominant role in determining the rate of net N mineralisation. Our findings also revealed soil substrate content (ammonium nitrogen and nitrite nitrogen, soil organic carbon, and C:N ratio) and soil environment (soil temperature and soil moisture) to be the major drivers of net N mineralisation in soil via their regulatory effects on the composition of microbial communities and functional genes. Our characterisation of the microbial metagenomic basis of net N mineralisation in forest soils accordingly highlights the importance of the combined contributions of soil microbial functional genes, soil substrate, and environmental factors in determining the cycling of N in forest soils at different elevations.Highlights Net N mineralisation rate followed a unimodal pattern along an elevational gradient. Denitrification and ammonia assimilation genes were correlated with net N mineralisation rate. Cyanobacteria play a dominant role in determining net N mineralisation rate. Soil substrate and environment determine microbial functional gene distribution.

Microbial behaviours inside alternating anaerobic-anoxic environment of a sulfur cycle–driven EBPR system: A metagenomic investigation

Denitrifying sulfur conversion-assisted enhanced biological phosphorus removal (DS-EBPR) was recently developed for saline wastewater treatment. However, the main functional bacteria and the interrelationship of functional bacteria of the DS-EBPR have not been defined and identified so far. This study used metagenomics and multivariate statistics to deduce the functional microbial community and distribution of functional genes associated with the critical metabolic pathways of carbon (C), nitrogen (N), phosphorus (P) and sulfur (S), particularly regarding how they would behave under the alternating anaerobic-anoxic conditions inside a long-term DS-EBPR system. An analysis of the metagenomics and metabolic functions identified 11 major microbial species which were classifiable into four groups: sulfate reducing bacteria (SRB, 0.8–2.2%), sulfur oxidizing bacteria (SOB, 31.9–37.7%), denitrifying phosphate accumulating organisms (DPAOs, 10.0–15.8%) and glycogen accumulating organisms (GAOs, 3.7–7.7%). The four groups of microorganisms performed their respective metabolisms synergistically. In terms of distribution of functional genes, SRB (Desulfococcus and Desulfobacter) and SOB (Chromatiaceae and Thiobacillus) are not only encoded by the related sulfur conversion genes (sqr, dsrAB, aprAB and sat), but also encoded by the necessary ppx and ppk1 gene for P removal that they can be considered as the potential S-related PAOs. Between the anaerobic and anoxic conditions, the metagenome-based microbial community remained structurally similar, but the functional genes, which encode various key enzymes for the P, N, and S pathways, changed in abundance. This study contributes to our understanding on the interactions and competition between the SRB, SOB, DPAOs, and GAOs in a DS-EBPR system.

Functional Genetic Diversity and Plant Growth Promoting Potential of Polyphosphate Accumulating Bacteria in Soil.

ABSTRACTPolyphosphate (polyP) accumulation is an important trait of microorganisms. Implication of polyP accumulating bacteria (PAB) in enhanced biological phosphate removal, heavy metal sequestration, and dissolution of dental enamel is well studied. Phosphorous (P) accumulated within microbial biomass also regulates labile P in soil; however, abundance and diversity of the PAB in soil is still unexplored. Present study investigated the genetic and functional diversity of PAB in rhizosphere soil. Here, we report the abundance of Pseudomonas spp. as high PAB in soil, suggesting their contribution to global P cycling. Additional subset analysis of functional genes i.e., polyphosphate kinase (ppk) and exopolyphosphatase (ppx) in all PAB, indicates their significance in bacterial growth and metabolism. Distribution of functional genes in phylogenetic tree represent a more biologically realistic discrimination for the two genes. Distribution of ppx gene disclosed its phylogenetic conservation at species level, however, clustering of ppk gene of similar species in different clades illustrated its environmental condition mediated modifications. Selected PAB showed tolerance to abiotic stress and strong correlation with plant growth promotary (PGP) traits viz. phosphate solubilization, auxin and siderophore production. Interaction of PAB with A. thaliana enhanced the growth and phosphate status of the plant under salinity stress, suggestive of their importance in P cycling and stress alleviation.IMPORTANCE Study discovered the abundance of Pseudomonas genera as a high phosphate accumulator in soil. The presence of functional genes (polyphosphate kinase [ppk] and exopolyphosphatase [ppx]) in all PAB depicts their importance in polyphosphate metabolism in bacteria. Genetic and functional diversity reveals conservation of the ppx gene at species level. Furthermore, we found a positive correlation between PAB and plant growth promotary traits, stress tolerance, and salinity stress alleviation in A. thaliana.

Bacterial community structure and putative nitrogen-cycling functional traits along a charosphere gradient under waterlogged conditions

Unique spatial niches created by biochar form a dynamic biogeochemical soil zone, termed the “charosphere”. Charosphere soil has different properties from either soil or biochar, often acting as a hotspot for microbial activity. However, the direction and magnitude of charosphere effects on soil processes and microbial communities remain inconclusive. Herein, we designed a multi-sectional box to separate charosphere soils from biochar under waterlogged conditions, investigating millimeter-scale changes in bacterial communities and distributions of specific genera across the charosphere created by pristine biochar (produced from corn stover at 300 °C), acid-modified biochar and washed biochar. The pristine biochar did not increase bacterial α-diversity but altered bacterial composition by promoting the growth of specific bacterial taxa and suppressing other species. In comparison, washed and acid-modified biochar increased the bacterial α-diversity. The pristine biochar significantly decreased N2O emission and NO3− concentration owing to a lower soil nitrification potential. Abundances of N-cycling functional taxa were higher in the near-charosphere than outer-charosphere zone, especially for Bacillus (N2-fixation), MND1 (ammonia oxidation) and Rhodopseudomonas (denitrification). The spatial distribution of functional genes and genera documents the importance of heterogeneity within the charosphere gradient, providing a novel perspective into functional geometry to understand how biochar reduces N losses from agroecosystems.

Insights into microbial actions on hydraulic concrete structures: Effects of concrete alkalinity on bacterial community composition and functional expression

Microbial induced concrete degradation (MICD) has received increased research attention. Nonetheless, microbial actions on hydraulic concrete structures (HCSs) in freshwater are poorly understood compared with those in sewer systems. Knowledge of the effects of the highly alkaline nature of concretes on attached microbial communities on HCSs is especially lacking. Here, we studied the composition and succession of bacterial communities in the deterioration layers of HCSs in response to concrete alkalinity gradients with the pH ranging from 7.88 to 12.08. Furthermore, variation in the functional bacteria potentially related to MICD was explored by functional prediction based on the Kyoto Encyclopedia of Genes and Genome (KEGG) pathways database. The diversities and abundances of most bacterial communities at the phylum and genus level were significantly inhibited by dosed alkalinity, and a positive relationship was observed between the abundance of Cyanobacteria and concrete alkalinity. The bacterial communities in attached biofilms gradually increased in similarity as succession progressed, whereas concrete alkalinity led to slight increases in the similarity in community structure. The main contribution of community assemblage was from a turnover pattern caused by species replacement. A nonlinear relationship was observed between concrete alkalinity and the distributions of functional genes related to nitrogen and sulfur metabolism. The distribution of functional genes was most affected by high alkalinity solutions (pH 11.39–12.08), whereas the distribution of functional genes was least affected by moderate alkalinity conditions (pH 10.88–11.16). The nitrogen cyclic pathways were dominated by partial ammonia oxidation, and self-assimilation was the major process in the sulfur metabolic cycle. As the alkalinity gradients decreased in strength, the biological activities of functional genes related to MICD gradually increased, potentially exacerbating microbial degradation on HCSs. Generally, our work provides new insight into the effects of concrete alkalinity on microbial actions and improves our understanding of the safety and durability of water conservation projects in marine and freshwater environments with high alkalinity.

Functional Associations and Resilience in Microbial Communities.

Microbial communities have inherently high levels of metabolic flexibility and functional redundancy, yet the structure of microbial communities can change rapidly with environmental perturbation. To understand whether such changes observed at the taxonomic level translate into differences at the functional level, we analyzed the structure of taxonomic and functional gene distribution across Arctic and Antarctic locations. Taxonomic diversity (in terms of alpha diversity and species richness) differed significantly with location. However, we found that functional genes distributed evenly across bacterial networks and that this functional distribution was also even across different geographic locations. For example, on average 15% of the functional genes were related to carbon cycling across all bacterial networks, slightly over 21% of the genes were stress-related and only 0.5% of the genes were linked to carbon degradation functions. In such a distribution, each bacterial network includes all of the functional groups distributed following the same proportions. However, the total number of functional genes that is included in each bacterial network differs, with some clusters including many more genes than others. We found that the proportion of times a specific gene must occur to be linked to a specific cluster is 8%, meaning the relationship between the total number of genes in the cluster and the number of genes per function follows a linear pattern: smaller clusters require a gene to appear less frequently to get fixed within the cluster, while larger clusters require higher gene frequencies. We suggest that this mechanism of functional association between equally rare or equally abundant genes could have implications for ecological resilience, as non-dominant genes also associate in fully functioning ecological networks, potentially suggesting that there are always pre-existing functional networks available to exploit new ecological niches (where they can become dominant) as they emerge; for example, in the case of rapid or sudden environmental change. Furthermore, this pattern did not correlate with taxonomic distribution, suggesting that bacteria associate based on functionality and this is independent of its taxonomic position. Our analyses based on ecological networks also showed no clear evidence of recent environmental impact on polar marine microbial communities at the functional level, unless all communities analyzed have changed exactly in the same direction and intensity, which is unlikely given we are comparing areas changing at different rates.

Soil Microbial Community Assembly and Interactions Are Constrained by Nitrogen and Phosphorus in Broadleaf Forests of Southern China

Subtropical and tropical broadleaf forests play important roles in conserving biodiversity and regulating global carbon cycle. Nonetheless, knowledge about soil microbial diversity, community composition, turnover and microbial functional structure in sub- and tropical broadleaf forests is scarce. In this study, high-throughput sequencing was used to profile soil microbial community composition, and a micro-array GeoChip 5.0 was used to profile microbial functional gene distribution in four sub- and tropical broadleaf forests (HS, MES, HP and JFL) in southern China. The results showed that soil microbial community compositions differed dramatically among all of four forests. Soil microbial diversities in JFL were the lowest (5.81–5.99) and significantly different from those in the other three forests (6.22–6.39). Furthermore, microbial functional gene interactions were the most complex and closest, likely in reflection to stress associated with the lowest nitrogen and phosphorus contents in JFL. In support of the importance of environmental selection, we found selection (78–96%) dominated microbial community assembly, which was verified by partial Mantel tests showing significant correlations between soil phosphorus and nitrogen content and microbial community composition. Taken together, these results indicate that nitrogen and phosphorus are pivotal in shaping soil microbial communities in sub- and tropical broadleaf forests in southern China. Changes in soil nitrogen and phosphorus, in response to plant growth and decomposition, will therefore have significant changes in both microbial community assembly and interaction.

Response of chemical properties, microbial community structure and functional genes abundance to seasonal variations and human disturbance in Nanfei River sediments

The Nanfei River, located in Hefei City, Anhui Province, subjected to increased nutrient loads from point and/or non-point source. Little is known about the indicators indicating heterogeneity of surface sediments. We aimed to identify the suitable indicators that can reflect the sediment heterogeneity by analyzing the sensitivity of sediment physicochemical properties group, microbial communities and diversity indices group and C, N, S-functional genes group to seasonal and regional changes. River sediments from different areas (urban area, urban-rural fringe and rural area) were collected in the level, dry and wet seasons, respectively. The chemical parameters had most significant regional heterogeneity, but no seasonal differences. Seasons had a greater impact on the overall microbial community structure than the areas. Specifically, the relative abundance of Firmicutes and Bacteroidetes were more sensitive to seasonal changes. Overall, seasonal changes showed the greatest impact on the functional genes group, with the S-functional genes (dsrB and aprA) group providing the clearest seasonal variation. Considering the seasonal distribution of functional genes and their sensitivity to environmental factors, we speculated that the sulfate-reducing gene (dsrB), the methanogenic gene (mcrA) and the anammox gene (hzo) could be identified as sensitive indicators to indicate the seasonal heterogeneity of surface sediments in different river sections of the same river in the short term. We also concluded that environmental variables were more conducive to indicating the regional heterogeneity of sediments. This study provided a valuable reference for assessing the heterogeneity or ecological stress of river sediments.

Bacterial community rather than metals shaping metal resistance genes in water, sediment and biofilm in lakes from arid northwestern China

Lakes in arid northwestern China are valuable freshwater resources that drive socioeconomic development. Environmental pollution can significantly influence the composition of microbial communities and the distribution of functional genes in lakes. This study investigated heavy metal pollution to identify possible correlations with metal resistance genes (MRGs) and bacterial community composition in water, sediment and biofilm samples from Bosten Lake and Ebi Lake in northwestern China. High levels of zinc were detected in all samples. However, the metals detected in the sediment samples of both lakes were determined to be at low risk levels according to an ecological index. The mercury resistance gene subtype merP had the greatest average abundance (4.61 × 10−3 copies per 16S rRNA) among all the samples, followed by merA and merC. The high abundance of merA in the pelagic zone rather than in benthic sediment suggests that the pelagic microbial community was important in mercury reduction. Proteobacteria were the main phylum found in the microbial communities in all samples. However, microbial communities in most of the water, sediment and biofilm samples had different compositions, indicating that the habitat niche plays an important role in shaping the bacterial communities in lakes. The microbial community, rather than the heavy metals, was the main driver of MRG distribution. The abundances of some bacterial genera involved in the decomposition of organic matter and the terrestrial nitrogen cycle were negatively correlated with heavy metals. This result suggests that metal pollution can adversely affect the biogeochemical processes that occur in lakes.

Mudflat reclamation causes changes of gene abundance in nitrogen cycle under long-term rice cultivation.

Rice cultivation is the main method for mudflat reclamation. However, changes in the community structure of microbes involved in nitrogen (N) cycling in response to mudflat reclamation via rice cultivation remain poorly understood. This study used quantitative polymerase chain reaction to characterize the distribution of various inorganic N-cycling pathways in response to mudflat reclamation via rice cultivation. The results show that the abundance of functional genes followed an increasing trend, while the relative abundance showed a decreasing trend. The relative richness of functional genes in the inorganic N-cycling network showed different fluctuation trends and indicated that the nifH, archaea amoA, narG, nirS, nirK, norB, and nosZ genes greatly contribute to inorganic N-cycling. Redundancy analysis showed that soil properties, in particular, organic matter increased, while electrical conductivity decreased, driving the changes of gene distribution in the inorganic N-cycling network over the course of reclamation. Mudflat reclamation under long-term rice cultivation promoted the reproduction of microbes related to the N cycle, and also changed the distribution of functional genes that are involved in the inorganic N cycle due to changes of soil properties.

Microbial functional genes elucidate environmental drivers of biofilm metabolism in glacier-fed streams

Benthic biofilms in glacier-fed streams harbor diverse microorganisms driving biogeochemical cycles and, consequently, influencing ecosystem-level processes. Benthic biofilms are vulnerable to glacial retreat induced by climate change. To investigate microbial functions of benthic biofilms in glacier-fed streams, we predicted metagenomes from 16s rRNA gene sequence data using PICRUSt and identified functional genes associated with nitrogen and sulfur metabolisms based on KEGG database and explored the relationships between metabolic pathways and abiotic factors in glacier-fed streams in the Tianshan Mountains in Central Asia. Results showed that the distribution of functional genes was mainly associated with glacier area proportion, glacier source proportion, total nitrogen, dissolved organic carbon, and pH. For nitrogen metabolism, the relative abundance of functional genes associated with dissimilatory pathways was higher than those for assimilatory pathways. The relative abundance of functional genes associated with assimilatory sulfate reduction was higher than those involved with the sulfur oxidation system and dissimilatory sulfate reduction. Hydrological factors had more significant correlations with nitrogen metabolism than physicochemical factors and anammox was the most sensitive nitrogen cycling pathway responding to variation of the abiotic environment in these glacial-fed streams. In contrast, sulfur metabolism pathways were not sensitive to variations of abiotic factors in these systems.

Analysis of functional genomes from metagenomes: Revealing the accelerated electron transfer in microbial fuel cell with rhamnolipid addition

Extracellular electron transfer is the predominant electricity generation process in microbial fuel cells (MFCs). Our pervious study have proved that the anodic adsorption of rhamnolipid resulted in the Frumkin effect, which enhanced anodic microorganism attachment and accelerated anodic electron transfer. In this study, an in-depth research on the influence of rhamnolipid on functional genes of anodic biofilms metagenomes was carried out to explain its mechanism at the gene level. The result showed that the composition and distribution of functional genes in each dominant genus were different. The category of signal transduction mechanisms was the dominant function category in exoelectrogens, and its relative abundance in the metagenome significantly increased from 4.56 to 5.86% from rhamnolipid addition. Additionally, the metabolic pathway and electron flow analysis revealed that electron flows tend to choose direct electron transfer in the presence of rhamnolipids, and resulting in the increase of Coulombic efficiency from 19.10±0.79% to 27.39±1.07%.