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The many functions of microbial communities emerge from a complex web of interactions between organisms and their environment. This poses a significant obstacle to engineering microbial consortia, hindering our ability to harness the potential of microorganisms for biotechnological applications. In this study, we demonstrate that the collective effect of ecological interactions between microbes in a community can be captured by simple statistical models that predict how adding a new species to a community will affect its function. These predictive models mirror the patterns of global epistasis reported in genetics, and they can be quantitatively interpreted in terms of pairwise interactions between community members. Our results illuminate an unexplored path to quantitatively predicting the function of microbial consortia from their composition, paving the way to optimizing desirable community properties and bringing the tasks of predicting biological function at the genetic, organismal, and ecological scales under the same quantitative formalism.

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BACKGROUND: Microbial functioning on marine plastic surfaces has been poorly documented, especially within cold climates where temperature likely impacts microbial activity and the presence of hydrocarbonoclastic microorganisms. To date, only two studies have used metaproteomics to unravel microbial genotype-phenotype linkages in the marine 'plastisphere', and these have revealed the dominance of photosynthetic microorganisms within warm climates. Advancing the functional representation of the marine plastisphere is vital for the development of specific databases cataloging the functional diversity of the associated microorganisms and their peptide and protein sequences, to fuel biotechnological discoveries. Here, we provide a comprehensive assessment for plastisphere metaproteomics, using multi-omics and data mining on thin plastic biofilms to provide unique insights into plastisphere metabolism. Our robust experimental design assessed DNA/protein co-extraction and cell lysis strategies, proteomics workflows, and diverse protein search databases, to resolve the active plastisphere taxa and their expressed functions from an understudied cold environment. RESULTS: For the first time, we demonstrate the predominance and activity of hydrocarbonoclastic genera (Psychrobacter, Flavobacterium, Pseudomonas) within a primarily heterotrophic plastisphere. Correspondingly, oxidative phosphorylation, the citrate cycle, and carbohydrate metabolism were the dominant pathways expressed. Quorum sensing and toxin-associated proteins of Streptomyces were indicative of inter-community interactions. Stress response proteins expressed by Psychrobacter, Planococcus, and Pseudoalteromonas and proteins mediating xenobiotics degradation in Psychrobacter and Pseudoalteromonas suggested phenotypic adaptations to the toxic chemical microenvironment of the plastisphere. Interestingly, a targeted search strategy identified plastic biodegradation enzymes, including polyamidase, hydrolase, and depolymerase, expressed by rare taxa. The expression of virulence factors and mechanisms of antimicrobial resistance suggested pathogenic genera were active, despite representing a minor component of the plastisphere community. CONCLUSION: Our study addresses a critical gap in understanding the functioning of the marine plastisphere, contributing new insights into the function and ecology of an emerging and important microbial niche. Our comprehensive multi-omics and comparative metaproteomics experimental design enhances biological interpretations to provide new perspectives on microorganisms of potential biotechnological significance beyond biodegradation and to improve the assessment of the risks associated with microorganisms colonizing marine plastic pollution. Video Abstract.

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Changes in soil microbial activity and ecological function can be used to assess the level of soil fertility and the stability of ecosystems. To assess the fertility and safety of organic fertilizer of kitchen waste (OFK), soils containing 0% (CK), 1%, 3%, and 5% OFK were cultured, and the physical, chemical, and microbial properties of the soils were measured dynamically with routine agrochemical analysis measures and amplicon sequencing. The results showed that compared with those in CK, the contents of organic matter, available phosphorus, available potassium, NH4+-N, and NO3--N in soils with OFK increased by 23.80%-35.13%, 13.29%-29.72%, 16.91%-39.37%, 164.7%-340.2%, and 28.56%-32.71%, respectively. The activities of hydrolases related to the cycle of carbon, nitrogen, and phosphorus (α-glucosidase, leucine aminopeptidase, acid phosphatase, etc.) were also significantly higher than those of the CK treatment. OFK stimulated the growth of soil microorganisms and increased the carbon content of the microbial biomass. The amplicon sequencing analysis found that the microbial community structures of different treatments were significantly different at both the class and genus levels. In addition, it was found that the abundance of beneficial microbes in the soils with OFK increased, whereas pathogenic microbes decreased. RDA results confirmed that soil properties (including soil pH, organic matter, available nutrients, and microbial biomass) had a significant impact on microbial community structure. The results of investing bacterial community based on PICRUSt and FAPROTAX revealed that the function of the soil bacterial community was similar in the four treatments, but OFK supply significantly improved the microbial carbon utilization and metabolic ability. Moreover, by using the FUNGuild software, we found that the application of OFK increased the proportion of saprotroph-symbiotroph and symbiotroph and stimulated the growth of ectomycorrhizal fungi-undefined saprophytic fungi but inhibited plant and animal pathogenic fungi in soil. These results implied that OFK could promote the establishment of symbiotic relationships and inhibit the growth of pathogenic fungi. In summary, OFK could improve soil fertility and hydrolase activity, stimulate the growth of beneficial microorganisms, and defend against pathogens, indicating a promising use as safe and efficient organic fertilizer.

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The addition of biochar in paddies under the condition of water-saving irrigation can simultaneously achieve soil improvement and water conservation, but little is known about the role of these two regulations in mediating the fate of antibiotic resistome in paddy soils. Here, metagenomic analysis was conducted to investigate the effects and intrinsic mechanisms of biochar application and irrigation patterns on propagation of antibiotic resistance genes (ARGs) in paddy soils. The addition of biochar in paddy soil resulted in a reduction of approximately 1.32%-8.01% in the total absolute abundance of ARGs and 0.60%-22.09% in the numbers of ARG subtype. Compared with flooding irrigation, the numbers of detected ARG subtype were reduced by 1.60%-22.90%, but the total absolute abundance of ARGs increased by 0.06%-5.79% in water-saving irrigation paddy soils. Moreover, the combined treatments of flooding irrigation and biochar could significantly reduce the abundance of ARGs in paddy soils. The incremental antibiotic resistance in soil induced by water-saving irrigation was likewise mitigated by the addition of biochar. Correlation analyses indicated that, the differences in soil physicochemical properties under biochar addition or irrigation treatments contributed to the corresponding changes in the abundance of ARGs. Moreover, the variations of microbial community diversity, multidrug efflux abundance and transport system-related genes in paddy soil were also important for mediating the corresponding differences in the abundance of ARGs under the conditions of biochar addition or irrigation treatments. The findings of this study demonstrated the effectiveness of biochar application in mitigating antibiotic resistance in paddy soils. However, it also highlighted a potential concern relating to the elevated antibiotic resistance associated with water-saving irrigation in paddy fields. Consequently, these results contribute to a deeper comprehension of the environmental risks posed by ARGs in paddy soils.

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Changes in land use strongly affect soil biological and physico-chemical structure and characteristics, which are strongly related to agricultural conversion of natural habitats to man-made usage. These are among the most important and not always beneficial changes, affecting loss of habitats. In Golan Heights basaltic soils, vineyards are currently a driving force in land-use change. Such changes could have an important effect on soil microbial community that play an important role in maintaining stable functioning of soil ecosystems. This study investigated the microbial communities in five different agro-managements using molecular tools that can clarify the differences in microbial community structure and function. Significant differences in soil microbial community composition were found. However, no differences in alpha diversity or functionality were found between the treatments. To the best of our knowledge, this is the first report indicating that the bacterial community in different agro-managements provide an insight into the potential function of a vineyard system.

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Soil microbial taxa have different functional ecological characteristics that influence the direction and intensity of plant-soil feedback responses to changes in the soil environment. However, the responses of soil microbial survival strategies to wet and dry events are poorly understood. In this study, soil physicochemical properties, enzyme activity, and high-throughput sequencing results were comprehensively anal0079zed in the irrigated cropland ecological zone of the northern plains of the Yellow River floodplain of China, where Oryza sativa was grown for a long period of time, converted to Zea mays after a year, and then Glycine max was planted. The results showed that different plant cultivations in a paddy-dryland rotation system affected soil physicochemical properties and enzyme activity, and G. max field cultivation resulted in higher total carbon, total nitrogen, soil total organic carbon, and available nitrogen content while significantly increasing α-glucosidase, ß-glucosidase, and alkaline phosphatase activities in the soil. In addition, crop rotation altered the r/K-strategist bacteria, and the soil environment was the main factor affecting the community structure of r/K-strategist bacteria. The co-occurrence network revealed the inter-relationship between r/K-strategist bacteria and fungi, and with the succession of land rotation, the G. max sample plot exhibited more stable network relationships. Random forest analysis further indicated the importance of soil electrical conductivity, total carbon, total nitrogen, soil total organic carbon, available nitrogen, and α-glucosidase in the composition of soil microbial communities under wet-dry events and revealed significant correlations with r/K-strategist bacteria. Based on the functional predictions of microorganisms, wet-dry conversion altered the functions of bacteria and fungi and led to a more significant correlation between soil nutrient cycling taxa and environmental changes. This study contributes to a deeper understanding of microbial functional groups while helping to further our understanding of the potential functions of soil microbial functional groups in soil ecosystems.

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The Antarctic marine environment is a dynamic ecosystem where microorganisms play an important role in key biogeochemical cycles. Despite the role that microbes play in this ecosystem, little is known about the genetic and metabolic diversity of Antarctic marine microbes. In this study we leveraged DNA samples collected by the Palmer Long Term Ecological Research (LTER) project to sequence shotgun metagenomes of 48 key samples collected across the marine ecosystem of the western Antarctic Peninsula (wAP). We developed an in silico metagenomics pipeline (iMAGine) for processing metagenomic data and constructing metagenome-assembled genomes (MAGs), identifying a diverse genomic repertoire related to the carbon, sulfur, and nitrogen cycles. A novel analytical approach based on gene coverage was used to understand the differences in microbial community functions across depth and region. Our results showed that microbial community functions were partitioned based on depth. Bacterial members harbored diverse genes for carbohydrate transformation, indicating the availability of processes to convert complex carbons into simpler bioavailable forms. We generated 137 dereplicated MAGs giving us a new perspective on the role of prokaryotes in the coastal wAP. In particular, the presence of mixotrophic prokaryotes capable of autotrophic and heterotrophic lifestyles indicated a metabolically flexible community, which we hypothesize enables survival under rapidly changing conditions. Overall, the study identified key microbial community functions and created a valuable sequence library collection for future Antarctic genomics research.

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As the widely used flame retardant, polybrominated diphenyl ethers (PBDEs) have been ubiquitously detected in wetland sediments. Microbial degradation is the importantly natural attenuation process for PBDEs in sediments. In this study, the microbial degradation of PBDEs and inherent alternation of microbial communities were explored in anaerobic sediments from coastal wetland, North China. BDE-47 and BDE-153 could be degraded by the indigenous microbes, with biodegradation following pseudo-first-order kinetic. In sediments, the major genera for BDE-47 and BDE-153 degradation were Paeisporosarcina and Gp7, respectively, in single exposure. However, Marinobacter was dominant genera in the combined exposure to BDE-47 and BDE-153, and competition against Marinobacter existed between BDE-47 and BDE-153 degradation. Analysis of bacterial metabolic function indicated that membrane transport, amino acid and carbohydrate metabolism were included in degradation. This study provides the systematic characterization of the sediment microbial community structure and function associated anaerobic microbial degradation of PBDEs in coastal wetland.

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Improper disposal of antibiotic fermentation dregs poses a risk of releasing antibiotics and antibiotic resistant bacteria to the environment. Therefore, this study evaluated the effects of biochar addition to lincomycin fermentation dregs (LFDs) composting. Biochar increased compost temperature and enhanced organic matter decomposition and residual antibiotics removal. Moreover, a 1.5- to 17.0-fold reduction in antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) was observed. Adding biochar also reduced the abundances of persistent ARGs hosts (e.g., Streptomyces, Pseudomonas) and ARG-related metabolic pathways and genes (e.g., ATP-binding cassette type-2 transport, signal transduction and multidrug efflux pump genes). By contrast, compost decomposition improved due to enhanced metabolism of carbohydrates and amino acids. Overall, adding biochar into LFDs compost reduced the proliferation of ARGs and enhanced microbial community metabolism. These results demonstrate that adding biochar to LFDs compost is a simple and efficient way to decrease risks associated with LFDs composting.

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Global nitrogen deposition has increased significantly in recent years. At present, research on the effects of different amounts and types of nitrogen deposition on soil microorganisms in coastal wetlands is scarce. In this study, based on 7 years of simulated nitrogen deposition at multiple levels (low, medium, high) and of multiple types (NH4NO3, NH4Cl, KNO3), the effects of different nitrogen deposition conditions on the diversity, community assembly processes, co-networks, and community function of soil prokaryotes in coastal wetlands were examined. The results showed that, compared with that in control, the microbial α diversity increased significantly under nitrogen deposition (P < 0.05). However, it decreased significantly in the high-NH4NO3 and high-NH4Cl treatments (P < 0.05). The deterministic process of community assembly was strengthened under the different types of nitrogen deposition. Compared with that under NH4+-N deposition, the microbial co-network under NO3--N deposition was more complex. Network stability significantly decreased under different NH4+-N deposition levels. In addition, the results of FAPROTAX functional prediction showed that microbial community functional groups associated with carbon and nitrogen cycling changed significantly (P < 0.05). In conclusion, our results emphasize that nitrogen deposition environments cause changes in soil microbial community structure and interactions, and may also affect soil carbon and nitrogen cycling, but the effects of different forms and levels of nitrogen deposition are not consistent. This study provides new insights for evaluating the changes in soil microbial communities in coastal wetlands caused by different types of long-term nitrogen deposition, and has scientific significance for assessing the ecological effects of long-term nitrogen deposition.

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Evaluating the potential alteration of microbial communities is a vital step for biosafety of genetic modified plants. Recently, we have produced genetic modified Ma bamboo with increased cold and drought tolerance by anthocyanin accumulation. In this work, we aim to study the potential effects on microbial communities in rhizosphere soils during the cultivation of genetic modified bamboo. Rhizosphere and surrounding soil were collected at 3-month post-transplant. The amplicon (16S rDNA and ITS1) were sequenced for analysis of bacterial and fungal communities. Multiple software and database (Picrust2, FAPROTAX and FUNGulid) were applied to predict and compare the microbial functions involving basic metabolisms, nitrogen usage and presence of plant pathogens. There were no substantial change of the structure and abundance of rhizosphere soil microbial communities between genetic modified and wild type bamboo. For the surrounding soil, the bacterial biota α-diversity increased (chao1: 1,001 ± 80-1,276 ± 84, observed species: 787 ± 52-1,194 ± 137, PD whole tree: 75 ± 4-117 ± 18) and fungal biota α-diversity decreased (chao1: 187 ± 18-145 ± 10) in samples of genetic modified bamboo compared to those of wild type bamboo. The microbiota predicted functions did not change or had no negative alteration between genetic modified and wild type bamboo, in both rhizosphere and surrounding soils. As a conclusion, the growth of genetic modified bamboo had no substantial change on rhizosphere soil microbial communities, while minor alteration on bamboo surrounding soil microbial communities with no harmful effects. Moreover, the genetic modified bamboo had no negative effect on the predicted functions of microbiota in soil.

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A membrane bioreactor with humic acid substrate (MBR-H) was operated to investigate organic removal and membrane performance. Approximately, 60% of chemical oxygen demand removal was observed in MBR-H. The biosorption capacity reached to the maximum value of 29.2 mg g-1 in the experiments with various activated sludge concentrations and the amount adsorbed on the newly produced microbes was limited. To understand key functions of microorganisms in the biodegradation of humic acid, the microbial community was examined. The dominant phylum was changed from Actinobacteria at the raw sludge to Proteobacteria at the MBR-H. Especially, great increases of ß-, γ-, and δ-Proteobacteria in the MBR-H indicated that those class of Proteobacteria played a vital role in humic acid removal. Investigation at the genus level showed enrichment of Stenotrophobacter in the MBR-H, which indicated the presence of metabolites in the proposed humic substance degradation pathway. In addition, the bacteria producing extracellular polymeric substances were increased in the MBR-H. Substantial variation of microbial community function was occurred in the MBR to degrade humic acid. Operational parameters in MBRs might be sought to maintain water permeability and to obtain preferable condition to evolution of microbial consortia for degradation of the refractory organic matter.

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Soil microorganisms, which are sensitive to environmental changes, affect soil nutrient cycling and play an important role in the biogeochemical cycling. To understand the changes of soil microorganisms in subtropical forest across the urban-rural environmental gradient, we analyzed the differences in soil microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), and microbial community functional diversitiy in Dashu Mountain National Forest Park (urban forest), Zipeng Mountain National Forest Park (suburban forest) in Hefei and Wanfo Mountain(rural forest) in Luan City. Results showed that soil MBC followed an order of rural natural forest (115.07 mg·kg-1) > suburban forest (101.68 mg·kg-1) > urban forest (82.73 mg·kg-1), soil MBN followed an order of rural natural forest (57.73 mg·kg-1) > urban forest (31.57 mg·kg-1) > suburban forest (29.01 mg·kg-1), soil microbial metabolic activities (AWCD), McIntosh index (U) were shown as rural natural forest > suburban forest > urban forest. The main carbon sources used by soil microbial communities in those forests were carboxylic acids, amino acids and carbohydrates, with weak utilization capacity for polyamines and polyphenols. The utilization capacity of soil microorganisms to amino acids, carboxylic acids, polymers and polyphenols followed the order of rural natural forest > suburban forest > urban forest. There were significant spatial variations in the functional characteristics of soil microbial communities under urban-rural environmental gradient, with Tween 80 and ß-methyl-D-Glucoside being the characteristic carbon sources as the influencing factors. Soil pH was significantly positively correlated with the microbial McIntosh index and AWCD value, while soil ammonium nitrogen (NH4+-N) showed a significant positive correlation with microbial Shannon diversity index and AWCD value. There was a negative correlation between the microbial Simpson index and soil nitrate nitrogen (NO3--N). Soil pH, NH4+-N and NO3--N were the main factors affecting diversity index of microbial communities. The results suggested that there were significant differences in microbial community characteristics of forest soil in urban-rural environmental gradient forests, and that the metabolic potential and functional diversity of soil microbial community in urban forests were weaker than that of natural forests.

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Tetracycline hydrochloride (TCH), as a typical antibiotic-pollutant, is desired to enhance its removal from public environment, due to its toxicity and persistence. Microbial electrochemical technology (MET) is a series complex microorganisms-driven processes with characteristics of simultaneous wastewater treatment and electricity generation. The study was presented to evaluate the TCH removal behavior and power generation performance through the co-metabolism under constant glucose with different TCH concentrations using MET. It was found that the TCH removal efficiency arrived at 40% during the first 6 h, when TCH concentrations ranged from 1 to 50 mg/L. It was interesting that TCH degradation rate increased to a maximum of 4.15 × 10-2 h-1 with its concentrations varying from 1 to 20 mg/L, however, the further increase to 50 mg/L in TCH concentration resulted in a reverse 66% reduction. In the meantime, the generated bioelectricity declared a similar fluctuation trend with a maximum power density of 600 mW/m2 under the condition of 20 mg/L TCH co-degradation with glucose. What's more, the TCH inhibition effect fitted well with Haldane's model, indicating that the microbial electrochemical system had a better potency toward TCH toxicity than that reported (EC50 = 2.2 mg/L). Thauera as mainly functional aromatics-degrading bacteria and Bdellovibrio against bacterial pathogens, only existed in the mixed cultures with TCH and glucose, indicating extremely remarkable changes in bacterial community with TCH addition. In summary, a new approach for the anaerobic biodegradation of TCH was explored through co-metabolism with glucose using MET. The results should be useful for antibiotics wastewater disposal of containing TCH.

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A 3-year pot experiment was carried out to investigate the efficiencies of hydroxyapatite (H), thiol-functionalized bentonite (T) and biochar (B) alone or in combination in remedying a Cd-Pb-contaminated soil. The application of passivating agents reduced the Cd and Pb mobility in acidic soil and enhanced soil microbial community function. The largest reductions in the Cd and Pb acid-soluble portions were observed under H (33.49%, 37.37%) and hydroxyapatite + thiol-functionalized bentonite + biochar (HTB, 36.70%, 37.31%), respectively. Biological analysis indicated that the AWCD (average well color development) of the B and HTB amendments was 1.42 and 1.51 times higher, respectively, than of untreated soil at 192 h. Moreover, the Shannon-Wiener, Simpson and Pielou indices were significantly increased in these two treatments relative to the values in the other amendment treatments. Therefore, combination amendments, such as HTB, which can reduce the bioavailability of both Cd and Pb and increase soil microbial activity, are recommended for practical applications.

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Mono-cultured and mix-cultured duckweed species were investigated with respect to the function of their associated microbial communities in heavy metal contaminated wastewater. Results show that the carbon source utilization patterns of the L. aequinoctialis- and S. polyrhiza-associated microbial communities were different. The relationships between microbial activity, antioxidant enzyme activity (CAT, GSH, and SOD) and growth was positive and significant. The microbial activity of L. aequinoctialis and S. polyrhiza in mixture was higher than in monoculture in low and high heavy metal, respectively, thereby altering the utilization of specific carbon source types and increasing duckweed growth and antioxidant enzyme activity, when compared to the monocultured duckweed. Furthermore, results indicate that duckweed species in mixture are protected from damage through regulation of the associated bacterial communities.

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Aerobic granular sludge (AGS), a self-immobilized microbial consortium containing different functional microorganisms, is receiving growing attention, since it has shown great technological and economical potentials in the field of wastewater treatment. Microbial community is crucial for the formation, stability, and pollutant removal efficiency of aerobic granules. This mini-review systematically summarizes the recent findings of the microbial community structure and function of AGS and discusses the new research progress in the microbial community dynamics during the granulation process and spatial distribution patterns of the microbiota in AGS. The presented information may be helpful for the in-depth theoretical study and practical application of AGS technology in the future.

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Wetland ecosystems are important reservoirs of biodiversity and significantly contribute to emissions of the greenhouse gases CO2, N2O, and CH4. High anthropogenic nitrogen (N) inputs from agriculture and fossil fuel combustion have been recognized as a severe threat to biodiversity and ecosystem functioning, such as control of greenhouse gas emissions. Therefore, it is important to understand how increased N input into pristine wetlands affects the composition and activity of microorganisms, especially in interaction with dominant wetland plants. In a series of incubations analyzed over 90 days, we disentangled the effects of N fertilization on the microbial community in bulk soil and the rhizosphere of Juncus acutiflorus, a common and abundant graminoid wetland plant. We observed an increase in greenhouse gas emissions when N is increased in incubations with J. acutiflorus, changing the system from a greenhouse gas sink to a source. Using 16S rRNA gene amplicon sequencing, we determined that the bacterial orders Opitutales, subgroup 6 Acidobacteria, and Sphingobacteriales significantly responded to high N availability. Based on metagenomic data, we hypothesize that these groups are contributing to the increased greenhouse gas emissions. These results indicated that increased N input leads to shifts in microbial activity within the rhizosphere, altering N cycling dynamics. Our study provides a framework for connecting environmental conditions of wetland bulk and rhizosphere soil to the structure and metabolic output of microbial communities. IMPORTANCE Microorganisms living within the rhizospheres of wetland plants significantly contribute to greenhouse gas emissions. Understanding how microbes produce these gases under conditions that have been imposed by human activities (i.e., nitrogen pollution) is important to the development of future management strategies. Our results illustrate that within the rhizosphere of the wetland plant Juncus acutiflorus, physiological differences associated with nitrogen availability can influence microbial activity linked to greenhouse gas production. By pairing taxonomic information and environmental conditions like nitrogen availability with functional outputs of a system such as greenhouse gas fluxes, we present a framework to link certain taxa to both nitrogen load and greenhouse gas production. We view this type of combined information as essential in moving forward in our understanding of complex systems such as rhizosphere microbial communities.

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The effects of environmental factors on water microbial communities have been extensively studied, but little is known about the effects in shrimp cultural enclosure ecosystems. We analyzed 16S rRNA gene amplicons to determine the principal environmental factors that shape the structure and function of microbial communities in shrimp cultural enclosure ecosystems from Guangdong and Hainan provinces, in China. High quality sequences were clustered into operational taxonomic units (OTUs) at the 97% similarity level, generating 659-1,835 OTUs per sample. The 10 most abundant phyla were Proteobacteria, Bacteroidetes, Cyanobacteria, Planctomycetes, Actinobacteria, Verrucomicrobia, Firmicutes, Chlorobi, Chloroflexi, and Chlamydiae. The results of canonical correspondence analyses (CCA) indicated that salinity, total phosphate (TP), total nitrogen (TN), temperature, and pH were the most important factors shaping microbial community structure. Differences in microbial community structure between high and low salinity samples were explained by changes in the relative abundances of some OTUs (e.g., OTU5, OTU19, OTU21, OTU39, and OTU71). Moreover, the contribution of spatial distribution to the microbial community assembly was investigated via aggregated boosted tree (ABT) analyses, and the results indicated spatial isolation was not a major factor affecting the phylogenetic diversity and phylotypes of water microbial communities. Furthermore, we predicted water microbial community functional profiling using the PICRUSt program and principal component analyses (PCA) suggested that salinity was a major contributor to the structure and function of the microbial communities. Collectively, these results showed that environmental factors influenced the structure and function of water microbial communities, while salinity was the principal environmental factor instead of temperature, TP, TN, and pH in shrimp cultural enclosure ecosystems.

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Although the taxonomical/phylogenetic diversity of microbial communities in biological heap leaching systems has been investigated, the diversity of functional genes was still unclear, and, especially, the differentiation and the relationships of diversity and functions of microbial communities in leaching heap (LH) and leaching solution (LS) were also still unclear. In our study, a functional gene array (GeoChip 5.0) was employed to investigate the functional gene diversity, and 16S rRNA gene sequencing was used to explore the taxonomical/phylogenetic diversity of microbial communities in LH and LS subsystems of Dexing copper mine (Jiangxi, China). Detrended correspondence analysis (DCA) showed that both functional gene structure and taxonomical/phylogenetic structure of microbial communities were significantly different between LH and LS. Signal intensities of genes, including genes for sulfur oxidation (e.g., soxB), metal homeostasis (e.g., arsm), carbon fixation (e.g., rubisco), polyphosphate degradation (e.g., ppk), and organic remediation (e.g., hydrocarbons) were significantly higher in LH, while signal intensities of genes for carbon degradation (e.g., amyA), polyphosphate synthesis (e.g., ppx), and sulfur reduction (e.g., dsrA) were significantly higher in LS. Further inspection revealed that microbial communities in LS and LH were dominated by Acidithiobacillus and Leptospirillum. However, rare species were relatively higher abundant in LH. Additionally, diversity index of functional genes was significantly different in LS (9.915 ± 0.074) and LH (9.781 ± 0.165), and the taxonomical/phylogenetic diversity index was also significantly different in LH (4.398 ± 0.508) and LS (3.014 ± 0.707). Functional tests, including sulfur-oxidizing ability, iron-oxidizing ability, and pyrite bioleaching ability, showed that all abilities of microbial communities were significantly stronger in LH than those in LS. Further studies found that most key genes (e.g., soxC and dsrA), rather than functional gene diversity index, were significantly correlated with abilities of microbial communities by linear regression analysis and Pearson correlation tests. In addition, the abilities were significantly correlated with taxonomical/phylogenetic diversity index and some rare species (e.g., Ferrithrix).

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