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Ocean acidification (OA), a consequence of increased global carbon dioxide (CO2) emissions, is considered a major threat to marine ecosystems. Its effects on bacterioplankton activity, diversity, and community composition have received considerable attention. However, the direct impact of OA on heterotrophic bacterioplankton is often masked by the significant response of phytoplankton due to the close coupling of heterotrophic bacterioplankton and autotrophs. Here we investigated the responses of a heterotrophic bacterioplankton assemblage to high pCO2 (790-ppm) treatment in warm tropical western Pacific waters by conducting a microcosm experiment in dark for 12 days. Heterotrophic bacterioplankton abundance and production were enhanced by OA over the first 6 days of incubation, while the diversity and species richness were negatively affected. Bacterioplankton community composition in the high pCO2 treatment changed faster than that in the control. The molecular ecological network analysis showed that the elevated CO2 changed the overall connections among the bacterial community and resulted in a simple network under high CO2 condition. Species-specific responses to OA were observed and could be attributed to the different life strategies and to the ability of a given species to adapt to environmental conditions. In addition, high-throughput functional gene array analysis revealed that genes related to carbon and nitrogen cycling were positively affected by acidification. Together, our findings suggest that OA has direct effects on heterotrophic bacterioplankton in a low-latitude warm ocean and may therefore affect global biogeochemical cycles.

Accurate climate projections require an understanding of the effects of warming on ecological communities and the underlying mechanisms that drive them1–3. However, little is known about the effects of climate warming on the succession of microbial communities4,5. Here we examined the temporal succession of soil microbes in a long-term climate change experiment at a tall-grass prairie ecosystem. Experimental warming was found to significantly alter the community structure of bacteria and fungi. By determining the time-decay relationships and the paired differences of microbial communities under warming and ambient conditions, experimental warming was shown to lead to increasingly divergent succession of the soil microbial communities, with possibly higher impacts on fungi than bacteria. Variation partition- and null model-based analyses indicate that stochastic processes played larger roles than deterministic ones in explaining microbial community taxonomic and phylogenetic compositions. However, in warmed soils, the relative importance of stochastic processes decreased over time, indicating a potential deterministic environmental filtering elicited by warming. Although successional trajectories of microbial communities are difficult to predict under future climate change scenarios, their composition and structure are projected to be less variable due to warming-driven selection.

Background and aims: Exploring biodiversity linkages between aboveground and belowground biota is a core topic in ecology, and can have implications on our understanding of ecosystem process stability. Yet, this topic still remains underexplored. Here, we explored diversity linkages, in terms of both alpha- and beta- diversity, between plant and top soil microbial communities in a semi-arid grassland ecosystem. Methods: Soil microbial community structure was assessed based on both 16S rRNA and functional genes, and plant community composition was evaluated by traditional “species composition” and a newly-defined “biomass composition”, which includes the information on the biomass of each species. Results: The bacterial alpha-diversity, expressed as the richness and Shannon diversity of 16S rRNA genes, was significantly correlated with plant species richness and Shannon diversity, whereas the alpha-diversity of microbial functional genes showed marginal association with total plant biomass. Microbial beta-diversity, evaluated by 16S rRNA genes, showed close relationship with plant beta-diversity estimated by both “species composition” and “biomass composition”, while the microbial beta-diversity based on functional genes was only associated with the compositional variation in aboveground plant biomass. Conclusions: These results showed that the differences in metabolic potential of soil microbial communities, which is closely related with ecosystem functions, can be better predicted by the variation of plant-derived resources returned to soil, than merely by the species composition of the macro-organism communities.

It has been rarely questioned as to whether the enrichment of specific bacterial taxa found in the rhizosphere of a given plant species changes with different soil types under field conditions and under similar climatic conditions. Understanding tree microbiome interactions is essential because, in contrast to annual plants, tree species require decades to grow and strongly depend on the nutritive resources of the soil. In this context, we tested using a natural toposequence the hypothesis that beech trees select specific taxa and functions in their rhizosphere based on the soil conditions and their nutritive requirements. Our 16S rRNA gene pyrosequencing analyses revealed that the soil type determines the taxa colonizing the beech rhizosphere. A rhizosphere effect was observed in each soil type, but a stronger effect was observed in the nutrient-poor soils. Although the communities varied significantly across the toposequence, we identified a core beech rhizosphere microbiome. Functionally, GeoChip analyses showed a functional redundancy across the toposequence, with genes related to nutrient cycling and to the bacterial immune system being significantly enriched in the rhizosphere. Altogether, the data suggest that, regardless of the soil conditions, trees enrich variable bacterial communities to maintain the functions necessary for their nutrition.

A railroad causeway across Great Salt Lake, Utah (GSL), has restricted water flow since its construction in 1959, resulting in a more saline North Arm (NA; 24%-31% salinity) and a less saline South Arm (SA; 11%-14% salinity). Here, we characterized microbial carbonates collected from the SA and the NA to evaluate the effect of increased salinity on community composition and abundance and to determine whether the communities present in the NA are still actively precipitating carbonate or if they are remnant features from prior to causeway construction. SSU rRNA gene abundances associated with the NA microbialite were three orders of magnitude lower than those associated with the SA microbialite, indicating that the latter community is more productive. SSU rRNA gene sequencing and functional gene microarray analyses indicated that SA and NA microbialite communities are distinct. In particular, abundant sequences affiliated with photoautotrophic taxa including cyanobacteria and diatoms that may drive carbonate precipitation and thus still actively form microbialites were identified in the SA microbialite; sequences affiliated with photoautotrophic taxa were in low abundance in the NA microbialite. SA and NA microbialites comprise smooth prismatic aragonite crystals. However, the SA microbialite also contained micritic aragonite, which can be formed as a result of biological activity. Collectively, these observations suggest that NA microbialites are likely to be remnant features from prior to causeway construction and indicate a strong decrease in the ability of NA microbialite communities to actively precipitate carbonate minerals. Moreover, the results suggest a role for cyanobacteria and diatoms in carbonate precipitation and microbialite formation in the SA of GSL.

Management of soil biological resources to optimise plant production, efficiency of nutrient inputs, and system sustainability is an emerging opportunity for pastoral agriculture. To achieve these goals, suitable tools that can assess the functional state of the soil ecosystem must be developed and standardised approaches to their application adopted. Towards this end, we have undertaken comprehensive, high-density functional-gene microarray analysis (GeoChip5) of environmental DNA (eDNA) extracted from 50 pastoral soils. When combined with soil, environmental and management metadata, the information can be used to provide insights into soil biological processes spanning greenhouse gas emissions, through to natural suppression of plant root diseases. To provide an example of a structured workflow of analysis in a pastoral system context, we analysed the GeoChip data using a combination of approaches spanning routine univariate methods through to more complex multivariate and network-based analysis. Analyses were restricted to comparing effects of land-use (dairy or ‘other’ farming systems), and exploring relationships of the GeoChip data with the soil properties from each sample. These exemplar analyses present a pathway for the application of eDNA approaches (GeoChip or others) to deliver outcomes for pastoral agricultural in New Zealand.

Microbial decomposition of soil carbon in high-latitude tundra underlain with permafrost is one of the most important, but poorly understood, potential positive feedbacks of greenhouse gas emissions from terrestrial ecosystems into the atmosphere in a warmer world. Using integrated metagenomic technologies, we showed that the microbial functional community structure in the active layer of tundra soil was significantly altered after only 1.5 years of warming, a rapid response demonstrating the high sensitivity of this ecosystem to warming. The abundances of microbial functional genes involved in both aerobic and anaerobic carbon decomposition were also markedly increased by this short-term warming. Consistent with this, ecosystem respiration (R eco) increased up to 38%. In addition, warming enhanced genes involved in nutrient cycling, which very likely contributed to an observed increase (30%) in gross primary productivity (GPP). However, the GPP increase did not offset the extra R eco, resulting in significantly more net carbon loss in warmed plots compared with control plots. Altogether, our results demonstrate the vulnerability of active-layer soil carbon in this permafrost-based tundra ecosystem to climate warming and the importance of microbial communities in mediating such vulnerability.

Ocean acidification (OA), caused by seawater CO2 uptake, has significant impacts on marine calcifying organisms and phototrophs. However, the response of bacterial communities, who play a crucial role in marine biogeochemical cycling, to OA is still not well understood. Previous studies have shown that the diversity and structure of microbial communities change undeterminably with elevated pCO2. Here, novel phylogenetic molecular ecological networks (pMENs) were employed to investigate the interactions of native bacterial communities in response to OA in the Arctic Ocean through a mesocosm experiment. The pMENs results were in line with the null hypothesis that elevated pCO2/pH does not affect biogeochemistry processes. The number of nodes within the pMENs and the connectivity of the bacterial communities were similar, despite increased pCO2 concentrations. Our results indicate that elevated pCO2 did not significantly affect microbial community structure and succession in the Arctic Ocean, suggesting bacterioplankton community resilience to elevated pCO2. The competitive interactions among the native bacterioplankton, as well as the modular community structure, may contribute to this resilience. This pMENs-based investigation of the interactions among microbial community members at different pCO2 concentrations provides a new insight into our understanding of how OA affects the microbial community.

Understanding the influence of long-term crop management practices on the soil microbial community is critical for linking soil microbial flora with ecosystem processes such as those involved in soil carbon cycling. In this study, pyrosequencing and a functional gene array (GeoChip 4.0) were used to investigate the shifts in microbial composition and functional gene structure in a medium clay soil subjected to various cropping regimes. Pyrosequencing analysis showed that the community structure (β-diversity) for bacteria and fungi was significantly impacted among different cropping treatments. Functional gene array-based analysis revealed that crop rotation practices changed the structure and abundance of genes involved in C degradation. Significant correlations were observed between the activities of four enzymes involved in soil C degradation and the abundance of genes responsible for the production of respective enzymes, suggesting that a shift in the microbial community may influence soil C dynamics. We further integrated physical, chemical, and molecular techniques (qPCR) to assess relationships between soil C, microbial derived enzymes and soil bacterial community structure at the soil micro-environmental scale (e.g. within different aggregate-size fractions). We observed a dominance of different bacterial phyla within soil microenvironments which was correlated with the amount of C in the soil aggregates suggesting that each aggregate represents a different ecological niche for microbial colonization. Significant effects of aggregate size were found for the activity of enzymes involved in C degradation suggesting that aggregate size distribution influenced C availability. The influence of cropping regimes on microbial and soil C responses declined with decreasing size of soil aggregates and especially with silt and clay micro-aggregates. Our results suggest that long term crop management practices influence the structural and functional potential of soil microbial communities and the impact of crop rotations on soil C turnover varies between different sized soil aggregates. These findings provide a strong framework to determine the impact of management practices on soil C and soil health.

Community assembly describes how different ecological processes shape microbial community composition and structure. How environmental factors impact community assembly remains elusive. Here we sampled microbial communities and >200 biogeochemical variables in groundwater at the Oak Ridge Field Research Center, a former nuclear waste disposal site, and developed a theoretical framework to conceptualize the relationships between community assembly processes and environmental stresses. We found that stochastic assembly processes were critical (>60% on average) in shaping community structure, but their relative importance decreased as stress increased. Dispersal limitation and 'drift' related to random birth and death had negative correlations with stresses, whereas the selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum. Assembly mechanisms also varied greatly among different phylogenetic groups. Our findings highlight the importance of microbial dispersal limitation and environmental heterogeneity in ecosystem restoration and management., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Importance: Amplicon sequencing of targeted genes is the predominant approach to estimate the membership and structure of microbial communities. However, accurate reconstruction of community composition is difficult due to sequencing errors, and other methodological biases and effective approaches to overcome these challenges are essential. Using a mock community of 33 phylogenetically diverse strains, this study evaluated the effect of GC content on sequencing results and tested different approaches to improve overall sequencing accuracy while characterizing the pros and cons of popular amplicon sequence data processing approaches. The sequencing results from this study can serve as a benchmarking data set for future algorithmic improvements. Furthermore, the new insights on sequencing error, chimera formation, and GC bias from this study will help enhance the quality of amplicon sequencing studies and support the development of new data analysis approaches., Competing Interests: The authors declare no conflict of interest.

Bacillus cereus strain CPT56D-587-MTF (CPTF) was isolated from the highly contaminated Oak Ridge Reservation (ORR) subsurface. This site is contaminated with high levels of nitric acid and multiple heavy metals. Amplicon sequencing of the 16S rRNA genes (V4 region) in sediment from this area revealed an amplicon sequence variant (ASV) with 100% identity to the CPTF 16S rRNA sequence. Notably, this CPTF-matching ASV had the highest relative abundance in this community survey, with a median relative abundance of 3.77% and comprised 20%-40% of reads in some samples. Pangenomic analysis revealed that strain CPTF has expanded genomic content compared to other B. cereus species-largely due to plasmid acquisition and expansion of transposable elements. This suggests that these features are important for rapid adaptation to native environmental stressors. We connected genotype to phenotype in the context of the unique geochemistry of the site. These analyses revealed that certain genes (e.g. nitrate reductase, heavy metal efflux pumps) that allow this strain to successfully occupy the geochemically heterogenous microniches of its native site are characteristic of the B. cereus species while others such as acid tolerance are mobile genetic element associated and are generally unique to strain CPTF., (© 2022 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.)

Short rotation coppice (SRC) is increasingly being adopted for bioenergy production, pollution remediation and land restoration. However, its long-term effects on soil microbial communities are poorly characterized. Here, we studied soil microbial functional genes and their biogeographic pattern under SRC with willow trees as compared to those under permanent grassland (C). GeoChip analysis showed a lower functional gene diversity in SRC than in C soil, whereas microbial ATP and respiration did not change. The SRC soil had lower relative abundances of microbial genes encoding for metal(-oid) resistance, antibiotic resistance and stress-related proteins. This indicates a more benign habitat under SRC for microbial communities after relieving heavy metal stress, consistent with the lower phytoavailability of some metals (i.e., As, Cd, Ni and Zn) and higher total organic carbon, NO 3 - -N and P concentrations. The microbial taxa-area relationship was valid in both soils, but the space turnover rate was higher under SRC within 0.125 m 2 , which was possibly linked to a more benign environment under SRC, whereas similar values were reached beyond thisarea. Overall, we concluded that SRC management can be considered as a phytotechnology that ameliorates the habitat for soil microorganisms, owing to TOC and nutrient enrichment on the long-term.

Microbial-mediated nitrate removal from groundwater is widely recognized as the predominant mechanism for nitrate attenuation in contaminated aquifers and is largely dependent on the presence of a carbon-bearing electron donor. The repeated exposure of a natural microbial community to an electron donor can result in the sustained ability of the community to remove nitrate; this phenomenon has been clearly demonstrated at the laboratory scale. However, in situ demonstrations of this ability are lacking. For this study, ethanol (electron donor) was repeatedly injected into a groundwater well (treatment) for six consecutive weeks to establish the sustained ability of a microbial community to remove nitrate. A second well (control) located upgradient was not injected with ethanol during this time. The treatment well demonstrated strong evidence of sustained ability as evident by ethanol, nitrate, and subsequent sulfate removal up to 21, 64, and 68%, respectively, as compared to the conservative tracer (bromide) upon consecutive exposures. Both wells were then monitored for six additional weeks under natural (no injection) conditions. During the final week, ethanol was injected into both treatment and control wells. The treatment well demonstrated sustained ability as evident by ethanol and nitrate removal up to 20 and 21%, respectively, as compared to bromide, whereas the control did not show strong evidence of nitrate removal (5% removal). Surprisingly, the treatment well did not indicate a sustained and selective enrichment of a microbial community. These results suggested that the predominant mechanism(s) of sustained ability likely exist at the enzymatic- and/or genetic-levels. The results of this study demonstrated the in situ ability of a microbial community to remove nitrate can be sustained in the prolonged absence of an electron donor., (© 2021 The Authors. Groundwater published by Wiley Periodicals LLC on behalf of National Ground Water Association.)

Soil organic matter is composed of a variety of carbon (C) forms. However, not all forms are equally accessible to soil microorganisms. Deprivation of C inputs will cause changes in the physical and microbial community structures of soils; yet the trajectories of such changes are not clear. We assessed microbial communities using phospholipid fatty acid profiling, metabarcoding, CO 2 emissions, and functional gene microarrays in a decade-long C deprivation field experiment. We also assessed changes in a range of soil physicochemical properties, including using X-ray Computed Tomography imaging to assess differences in soil structure. Two sets of soils were deprived of C inputs by removing plant inputs for 10 years and 1 year, respectively. We found a reduction in diversity measures, after 10 years of C deprivation, which was unexpected based on previous research. Fungi appeared to be most impacted, likely due to competition for scarce resources after exhausting the available plant material. This suggestion was supported by evidence of bioindicator taxa in non-vegetated soils that may directly compete with or consume fungi. There was also a reduction in copies of most functional genes after 10 years of C deprivation, though gene copies increased for phytase and some genes involved in decomposing recalcitrant C and methanogenesis. Additionally, soils under C deprivation displayed expected reductions in pH, organic C, nitrogen, and biomass as well as reduced mean pore size, especially in larger pores. However, pore connectivity increased after 10 years of C deprivation contrary to expectations. Our results highlight concurrent collapse of soil structure and biodiversity following long-term C deprivation. Overall, this study shows the negative trajectory of continuous C deprivation and loss of organic matter on a wide range of soil quality indicators and microorganisms., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 George, Fidler, Van Nostrand, Atkinson, Mooney, Creer, Griffiths, McDonald, Robinson and Jones.)

During the last several decades, viruses have been increasingly recognized for their abundance, ubiquity, and important roles in different ecosystems. Despite known contributions to aquatic systems, few studies examine viral abundance and community structure over time in terrestrial ecosystems. The effects of land conversion and land management on soil microbes have been previously investigated, but their effects on virus population are not well studied. This study examined annual dynamics of viral abundance in soils from a native tallgrass prairie and two croplands, conventional till winter wheat and no-till canola, in Oklahoma. Virus-like particle (VLP) abundance varied across sites, and showed clear seasonal shifts. VLP abundance significantly correlated with environmental variables that were generally reflective of land use, including air temperature, soil nitrogen, and plant canopy coverage. Structural equation modeling supported the effects of land use on soil communities by emphasizing interactions between management, environmental factors, and viral and bacterial abundance. Between the viral metagenomes from the prairie and tilled wheat field, 1,231 unique viral operational taxonomic units (vOTUs) were identified, and only five were shared that were rare in the contrasting field. Only 13% of the vOTUs had similarity to previously identified viruses in the RefSeq database, with only 7% having known taxonomic classification. Together, our findings indicated land use and tillage practices influence virus abundance and community structure. Analyses of viromes over time and space are vital to viral ecology in providing insight on viral communities and key information on interactions between viruses, their microbial hosts, and the environment. IMPORTANCE Conversion of land alters the physiochemical and biological environments by not only changing the aboveground community, but also modifying the soil environment for viruses and microbes. Soil microbial communities are critical to nutrient cycling, carbon mineralization, and soil quality; and viruses are known for influencing microbial abundance, community structure, and evolution. Therefore, viruses are considered an important part of soil functions in terrestrial ecosystems. In aquatic environments, virus abundance generally exceeds bacterial counts by an order of magnitude, and they are thought to be one of the greatest genetic reservoirs on the planet. However, data are extremely limited on viruses in soils, and even less is known about their responses to the disturbances associated with land use and management. The study provides important insights into the temporal dynamics of viral abundance and the structure of viral communities in response to the common practice of turning native habitats into arable soils.

Unraveling the succession of microbial communities is a core ecological research topic. Yet few studies have focused on how long-term secondary succession affects the functional profiles and ecological processes of abundant and rare microbial subcommunities. Here, we used amplicon sequencing and GeoChip analysis to explore the ecological functions of abundant and rare biospheres and their correlation with soil multinutrient cycling. Samples for this study were collected from a well-established secondary succession chronosequence that spans >30 years of dryland ecosystem development on the Loess Plateau of China. Although both abundant and rare subcommunities shifted with succession, the changing of beta-diversity of the microbial communities was primarily driven by species replacement of the rare biosphere. Phylogenetic changes of abundant and rare taxa were associated with their functional traits, which dominated the diversity-related selection along all succession ages. Neutral theory analysis indicated that the assemblage of abundant taxa over all successional ages was regulated by dispersal homogenizing and ecological drift. The null model revealed that homogeneous and variable selection were the dominant assembly processes for rare subcommunities compared with abundant species. pH and nitrogen content were the paramount drivers determining the assembly of microbial communities and functional genes, consistent with the importance of environmental filtering. Furthermore, the rare biosphere had a paramount role in the entire ecological network and was the major driver for most soil processes such as C, N, and S cycling. Nonetheless, a significant portion of soil P cycling was regulated by abundant taxa. Collectively, our study provides insight into the mechanisms underlying microbial community assembly and soil microbe-driven functional changes in biogeochemical processes during secondary succession., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Background: Travelers' diarrhea (TD) is common among military personnel deployed to tropical and subtropical regions. It remains unclear how TD and subsequent antibiotic treatment impact the resident microflora within the gut, especially given increased prevalence of antibiotic resistance among enteric pathogens and acquisition of multidrug-resistant organisms. We examined functional properties of the fecal microflora in response to TD, along with subsequent antibiotic treatment., Methods: Fecal samples from US and UK military service members deployed to Djibouti, Kenya, and Honduras who presented with acute watery diarrhea were collected. A sample was collected at acute presentation to the clinic (day 0, before antibiotics), as well as 7 and/or 21 days following a single dose of antibiotics (azithromycin [500 mg], levofloxacin [500 mg], or rifaximin [1650 mg], all with loperamide). Each stool sample underwent culture and TaqMan reverse transcription polymerase chain reaction analyses for pathogen and antibiotic resistance gene detection. Purified DNA from each sample was analyzed using the HumiChip3.1 functional gene array., Results: In total, 108 day 1 samples, 50 day 7 samples, and 94 day 21 samples were available for analysis from 119 subjects. Geographic location and disease severity were associated with distinct functional compositions of fecal samples. There were no overt functional differences between pre- and postantibiotic treatment samples, nor was there increased acquisition of antibiotic resistance determinants for any of the antibiotic regimens., Conclusions: These results indicate that single-dose antibiotic regimens may not drastically alter the functional or antibiotic resistance composition of fecal microflora, which should inform clinical practice guidelines and antimicrobial stewardship., Clinical Trials Registration Number: NCT01618591., (Published by Oxford University Press on behalf of Infectious Diseases Society of America 2021.)

Soil microorganisms are sensitive to temperature in cold ecosystems, but it remains unclear how microbial responses are modulated by other important climate drivers, such as precipitation changes. Here, we examine the effects of six in situ warming and/or precipitation treatments in alpine grasslands on microbial communities, plants, and soil carbon fluxes. These treatments differentially affected soil carbon fluxes, gross primary production, and microbial communities. Variations of soil CO 2 and CH 4 fluxes across all sites significantly ( r  >   0.70, P < 0.050) correlated with relevant microbial functional abundances but not bacterial or fungal abundances. Given tight linkages between microbial functional traits and ecosystem functionality, we conclude that future soil carbon fluxes in alpine grasslands can be predicted by microbial carbon-degrading capacities. IMPORTANCE The warming pace in the Tibetan Plateau, which is predominantly occupied by grassland ecosystems, has been 0.2°C per decade in recent years, dwarfing the rate of global warming by a factor of 2. Many Earth system models project substantial carbon sequestration in Tibet, which has been observed. Here, we analyzed microbial communities under projected climate changes by 2100. As the soil "carbon pump," the growth and activity of microorganisms can largely influence soil carbon dynamics. However, microbial gene response to future climate scenarios is still obscure. We showed that the abundances of microbial functional genes, but not microbial taxonomy, were correlated with carbon fluxes and ecosystem multifunctionality. By identifying microbial traits linking to ecosystem functioning, our results can guide the assessment of future soil carbon fluxes in alpine grasslands, a critical step toward mitigating climate changes., (Copyright © 2021 Qi et al.)

Soil aggregates, with complex spatial and nutritional heterogeneity, are clearly important for regulating microbial community ecology and biogeochemistry in soils. However, how the taxonomic composition and functional attributes of N-cycling-microbes within different soil particle-size fractions under a long-term fertilization treatment remains largely unknown. Here, we examined the composition and metabolic potential for urease activity, nitrification, N 2 O production and reduction of the microbial communities attached to different sized soil particles (2000-250, 250-53 and <53 μm) using a functional gene microarray (GeoChip) and functional assays. We found that urease activity and nitrification were higher in <53 μm fractions, whereas N 2 O production and reduction rates were greater in 2000-250 and 250-53 μm across different fertilizer regimes. The abundance of key N-cycling genes involved in anammox, ammonification, assimilatory and dissimilatory N reduction, denitrification, nitrification and N 2 -fixation detected by GeoChip increased as soil aggregate size decreased; and the particular key genes abundance (e.g., ureC, amoA, narG, nirS/K) and their corresponding activity were uncoupled. Aggregate fraction exerted significant impacts on N-cycling microbial taxonomic composition, which was significantly shaped by soil nutrition. Taken together, these findings indicate the important roles of soil aggregates in differentiating N-cycling metabolic potential and taxonomic composition, and provide empirical evidence that nitrogen metabolism potential and community are uncoupled due to aggregate heterogeneity., (© 2020 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Discerning the differences in activated sludge (AS) microbial community due to geographic location and environmental and operational factors is of great significance for precise design and maintenance of wastewater treatment plants (WWTPs). Hence, in this study, 150 AS samples collected from WWTPs in South China and North China were analyzed by 16 S rRNA gene sequencing. In general, AS microbial community in North China had lower diversity, higher proportions of stochastic assembly (35.7% v.s. 15.8%) and more network keystone species (19 v.s. 5) compared with southern AS community. Conductivity and SRT had significant effects on AS community in both regions. Latitude, annual mean temperature, and influent BOD, COD, and ammonia influenced South China community significantly, while pH and influent total phosphorus affected North China community. To achieve stable performance, southern WWTPs should carefully monitor fluctuations in wastewater characteristics, while northern WWTPs should monitor AS communities for shifts in the dominant taxa from immigrant strains brought in through the influent. Additionally, WWTPs in North China should be aware of the need to proactively control sludge bulking because of the high abundance and occurrence of Haliscomenobacter in these AS communities. MAIN FINDING: The call for regional design based on the regional discrepancy of microbial communities in activated sludge is uncovered and according suggestions were given., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Atmospheric CO 2 concentration is increasing, largely due to anthropogenic activities. Previous studies of individual free-air CO 2 enrichment (FACE) experimental sites have shown significant impacts of elevated CO 2 (eCO 2 ) on soil microbial communities; however, no common microbial response patterns have yet emerged, challenging our ability to predict ecosystem functioning and sustainability in the future eCO 2 environment. Here we analyzed 66 soil microbial communities from five FACE sites, and showed common microbial response patterns to eCO 2 , especially for key functional genes involved in carbon and nitrogen fixation (e.g., pcc/acc for carbon fixation, nifH for nitrogen fixation), carbon decomposition (e.g., amyA and pulA for labile carbon decomposition, mnp and lcc for recalcitrant carbon decomposition), and greenhouse gas emissions (e.g., mcrA for methane production, norB for nitrous oxide production) across five FACE sites. Also, the relative abundance of those key genes was generally increased and directionally associated with increased biomass, soil carbon decomposition, and soil moisture. In addition, a further literature survey of more disparate FACE experimental sites indicated increased biomass, soil carbon decay, nitrogen fixation, methane and nitrous oxide emissions, plant and soil carbon and nitrogen under eCO 2 . A conceptual framework was developed to link commonly responsive functional genes with ecosystem processes, such as pcc/acc vs. soil carbon storage, amyA/pulA/mnp/lcc vs. soil carbon decomposition, and nifH vs. nitrogen availability, suggesting that such common responses of microbial functional genes may have the potential to predict ecosystem functioning and sustainability in the future eCO 2 environment., (Copyright © 2020 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Elevated nitrate in the environment inhibits sulfate reduction by important microorganisms of sulfate-reducing bacteria (SRB). Several SRB may respire nitrate to survive under elevated nitrate, but how SRB that lack nitrate reductase survive to elevated nitrate remains elusive. To understand nitrate adaptation mechanisms, we evolved 12 populations of a model SRB (i.e., Desulfovibrio vulgaris Hildenborough, DvH) under elevated NaNO 3 for 1000 generations, analyzed growth and acquired mutations, and linked their genotypes with phenotypes. Nitrate-evolved (EN) populations significantly (p < 0.05) increased nitrate tolerance, and whole-genome resequencing identified 119 new mutations in 44 genes of 12 EN populations, among which six functional gene groups were discovered with high mutation frequencies at the population level. We observed a high frequency of nonsense or frameshift mutations in nitrosative stress response genes (NSR: DVU2543, DVU2547, and DVU2548), nitrogen regulatory protein C family genes (NRC: DVU2394-2396, DVU2402, and DVU2405), and nitrate cluster (DVU0246-0249 and DVU0251). Mutagenesis analysis confirmed that loss-of-functions of NRC and NSR increased nitrate tolerance. Also, functional gene groups involved in fatty acid synthesis, iron regulation, and two-component system (LytR/LytS) known to be responsive to multiple stresses, had a high frequency of missense mutations. Mutations in those gene groups could increase nitrate tolerance through regulating energy metabolism, barring entry of nitrate into cells, altering cell membrane characteristics, or conferring growth advantages at the stationary phase. This study advances our understanding of nitrate tolerance mechanisms and has important implications for linking genotypes with phenotypes in DvH.

An improved understanding of the diversity and composition of microbial communities carrying antibiotic resistance genes (ARGs) and virulence genes (VGs) in aquifers recharged with stormwater is essential to comprehend potential human health risks from water reuse. A high-throughput functional gene array was used to study the prevalence of ARGs and VGs in aquifer biofilms (n = 27) taken from three boreholes over three months. Bacterial genera annotated as opportunistic pathogens such as Aeromonas, Burkholderia, Pseudomonas, Shewanella, and Vibrio were ubiquitous and abundant in all biofilms. Bacteria from clinically relevant genera, Campylobacter, Enterobacter, Klebsiella, Mycobacterium, Mycoplasma, and Salmonella were detected in biofilms. The mean travel time of stormwater from the injection well to P1 and P3 boreholes was 260 and 360 days respectively. The presence of ARGs and VGs in the biofilms from these boreholes suggest a high spatial movement of ARGs and VGs in the aquifer. The ARGs with the highest abundance were small multidrug resistance efflux pumps (SMR) and multidrug efflux (Mex) followed by β-lactamase C genes. β- lactamase C encoding genes were primarily detected in Enterobacteriaceae, Pseudomonadaceae, Bacillaceae, and Rhodobacteraceae families. The VGs encoding siderophores, including aerobactin (iro and iuc genes), followed by pilin, hemolysin, and type III secretion were ubiquitous. Canonical correspondence analysis suggested that Total Organic Carbon (TOC), Dissolved Organic Carbon (DOC), turbidity, and Fe concentration has a significant impact on the microbial community structure of bacteria carrying ARGs and VGs. Post abstraction treatment of groundwater may be prudent to improve water security and reduce potential health risks., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Soil microbial respiration is an important source of uncertainty in projecting future climate and carbon (C) cycle feedbacks. However, its feedbacks to climate warming and underlying microbial mechanisms are still poorly understood. Here we show that the temperature sensitivity of soil microbial respiration (Q 10 ) in a temperate grassland ecosystem persistently decreases by 12.0 ± 3.7% across 7 years of warming. Also, the shifts of microbial communities play critical roles in regulating thermal adaptation of soil respiration. Incorporating microbial functional gene abundance data into a microbially-enabled ecosystem model significantly improves the modeling performance of soil microbial respiration by 5-19%, and reduces model parametric uncertainty by 55-71%. In addition, modeling analyses show that the microbial thermal adaptation can lead to considerably less heterotrophic respiration (11.6 ± 7.5%), and hence less soil C loss. If such microbially mediated dampening effects occur generally across different spatial and temporal scales, the potential positive feedback of soil microbial respiration in response to climate warming may be less than previously predicted.

Subsurface microbial communities mediate the transformation and fate of redox sensitive materials including organic matter, metals and radionuclides. Few studies have explored how changing geochemical conditions influence the composition of groundwater microbial communities over time. We temporally monitored alterations in abiotic forces on microbial community structure using 1L in-field bioreactors receiving background and contaminated groundwater at the Oak Ridge Reservation, TN. Planktonic and biofilm microbial communities were initialized with background water for 4 days to establish communities in triplicate control reactors and triplicate test reactors and then fed filtered water for 14 days. On day 18, three reactors were switched to receive filtered groundwater from a contaminated well, enriched in total dissolved solids relative to the background site, particularly chloride, nitrate, uranium, and sulfate. Biological and geochemical data were collected throughout the experiment, including planktonic and biofilm DNA for 16S rRNA amplicon sequencing, cell counts, total protein, anions, cations, trace metals, organic acids, bicarbonate, pH, Eh, DO, and conductivity. We observed significant shifts in both planktonic and biofilm microbial communities receiving contaminated water. This included a loss of rare taxa, especially amongst members of the Bacteroidetes, Acidobacteria, Chloroflexi, and Betaproteobacteria, but enrichment in the Fe- and nitrate- reducing Ferribacterium and parasitic Bdellovibrio. These shifted communities were more similar to the contaminated well community, suggesting that geochemical forces substantially influence microbial community diversity and structure. These influences can only be captured through such comprehensive temporal studies, which also enable more robust and accurate predictive models to be developed., Competing Interests: The authors have declared that no competing interests exist.

Short rotation coppice (SRC) with metal tolerant plants may attenuate the pollution of excessive elements with potential toxicity in soils, while preserving soil resources and functionality. Here, we investigated effects of 6 years phytomanagement with willow SRC on properties including heavy metal levels, toxicity tested by BioTox, microbial biomass, enzyme activities, and functional gene abundances measured by GeoChip of soils contaminated by As, Cd, Pb and Zn, as compared to the same soils under non-managed mixed grassland representing no intervention treatment (Unt). Though metal total concentrations did not differ by SRC and Unt, SRC soils had lower metal availability and toxicity, higher organic carbon, microbial biomass, phosphatase, urease and protease activities, as compared to Unt soils. Significantly reduced abundances of genes encoding resistances to various metals and antibiotics were observed in SRC, likely attributed to reduced metal selective pressure based on less heavy metal availability and soil toxicity. SRC also significantly reduced abundances of genes involved in nitrogen, phosphorus, and sulfur cycles, possibly due to the willow induced selection. Overall, while the SRC phytomanagement did not reduce the total heavy metal concentrations in soils, it decreased the heavy metal availability and soil toxicity, which in turn led to less metal selective pressure on microbial communities. The SRC phytomanagement also reduced the abundances of nutrient cycling genes from microbial communities, possibly due to intense plant nutrient uptake that depleted soil nitrogen and phosphorus availability, and thus site-specific practices should be considered to improve the soil nutrient supply for phytomanagement plants., (Copyright © 2020 Xue, Van Nostrand, Zhou, Neu, Müller, Giagnoni and Renella.)

Nitrous oxide (N 2 O) is an important greenhouse gas contributing to global climate change. Emissions of N 2 O from acidic forests are increasing rapidly; however, little is known about the mechanisms driving these emissions. We analyzed soil samples from a high N 2 O emission area (HEA, 224-601 μg N m -2  h -1 ) and an adjacent low emission area (LEA, 20-30 μg N m -2  h -1 ) of a highly acidified forest. HEA showed similar carbon and nitrogen (N) pools and microbial biomass to LEA, but significantly higher moisture and extractable nutrients than LEA did. GeoChip 4 detected 298 gene families (unadjusted P < 0.05; 94, adjusted P < 0.05) showing significantly different structures between HEA and LEA. Both areas had highly diverse N cycling functional genes. However, HEA had higher relative abundances of nor, P450nor, and archaeal nitrifier nirK, which provided evidence for the importance of denitrifiers in N 2 O emission. HEA also showed significantly higher relative abundances of lignin- and cellulose-degrading genes, oxygen-limitation-response genes and denitrifier ppk, but lower abundances of N- and phosphorus (P) -limitation-response genes especially denitrifier pstS, corresponding to the higher moisture and extractable nutrients conducive to denitrification. The moisture, extractable nutrients and pH explained over 50% variation in microbial communities, and extractable P appeared as the key factor driving community variation and consequently regulated N 2 O production. CAPSULE ABSTRACT: N 2 O emission in highly acidified forest soils was related to the diverse N functional genes, especially denitrification genes, and was affected by soil properties., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Scientific understanding of microbial biogeography and assembly is lacking for activated sludge microbial communities, even though the diversity of microbial communities in wastewater treatment plants (WWTPs) is thought to have a direct influence on system performance. Here, utilizing large-scale 16S rRNA gene data generated from 211 activated sludge samples collected from 15 cities across China, we show activated sludge microbes, whose growth and metabolism can be regulated followed with the metabolic theory of ecology with an apparent Ea value (apparent activation energy) of 0.08 eV. WWTPs at a lower latitude tend to harbor a more diverse array of microorganisms. In agreement with the general understanding, the activated sludge microbial assembly was mainly driven by deterministic processes and the mean annual temperature was identified as the most important factor affecting the microbial community structure. The treatment process types with similar microbial growth types and functions had a distinct impact on the activated sludge microbial community structure only when WWTPs were located near each other and received similar influent. Overall, these findings provide us with a deeper understanding of activated sludge microbial communities from an ecological perspective. Moreover, these findings suggest that, for a given set of performance characteristics (e.g., combined nitrification, denitrification, and phosphorus removal), it may be difficult to employ common engineering levers to control additional aspects of community structure due to the influence of natural environmental factors.

Wastewater treatment plants (WWTPs) are critical for maintaining sustainable development in modern societies, wherein microbial populations residing in activated sludge (AS) are responsible for the removal of pollutants from wastewater. The biodegradability [biological oxygen demand/chemical oxygen demand (B/C ratio)] of influent, as a measure of the degree of available energy and toxicity to microorganisms in AS, has been hypothesized to drive AS microbial community assembly. However, the validity of this hypothesis has not been tested in full-scale WWTPs. In this study, we assessed the pollutant removal loads, the microbial community diversity, the relative importance of deterministic and stochastic assembly processes, and bio-interactions within the communities by analyzing 195 AS samples comprising nearly 5 000 000 16S rRNA sequences. Our results indicate that the effects of B/C ratio on pollutant removal loads can be perfectly reflected through biological properties, implying that B/C ratio determined WWTPs performance through affecting microbial community. Very low and/or very high B/C ratios result in low microbial diversity, strong stochastic processes, and large, complex networks, leading to low pollutant removal load of treatment. A B/C ratio of around 0.5 was optimal for system stability and efficiency. Based on the results of this study, the authors propose using the B/C ratio as an indispensable index to assess system performance and to provide an indicator of an impending process upset before function deteriorates significantly. This study provides a specific measure that can be used to evaluate strategies for process optimization and operation of WWTPs., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

The increasing prevalence of antibiotic-resistant microorganisms imposes a global threat to public health. The over reliant use of antibiotics in the food industry has contributed considerably to the dissemination of antibiotics into various environments, yet the mechanisms by which antibiotic dissemination influences the assembly of the microbial community continues to remain obscure. Here, we examine bacterial and fungal community assemblies in swine manure, compost, compost amended, and unamended agricultural soil in five suburban areas of Beijing, China. Total antibiotic concentration decreased by factors of 10-1000 from manure and compost to soils. The bacterial α-diversity was found to be low in manure and compost samples, while the fungal α-diversity was similar across all samples. We detected significantly (p < 0.05) higher relative abundances of well recognized pathogenic microbial taxa, virulence associated genes, and antibiotic resistance genes (ARGs) in manure and compost than those in agricultural soils, revealing the higher microbial capacity of pathogenicity, virulence and antibiotic resistance. Unexpectedly, the relative abundances of both bacterial and fungal taxa did not predict the antibiotic concentration. A possible explanation was that bacterial and fungal communities were mainly shaped by random assemblies. Rather, antibiotic concentration could be well predicted by relative abundances of antibiotic resistance, stress and virulence associated genes. Despite the weak interconnection between ARGs and the microbiome, we demonstrate that microbial genes should be the focal point in tracking the ecological effects of antibiotic dissemination by revealing microbial community patterns along the dissemination chain of antibiotics., (Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Background: It is well-known that global warming has effects on high-latitude tundra underlain with permafrost. This leads to a severe concern that decomposition of soil organic carbon (SOC) previously stored in this region, which accounts for about 50% of the world's SOC storage, will cause positive feedback that accelerates climate warming. We have previously shown that short-term warming (1.5 years) stimulates rapid, microbe-mediated decomposition of tundra soil carbon without affecting the composition of the soil microbial community (based on the depth of 42684 sequence reads of 16S rRNA gene amplicons per 3 g of soil sample)., Results: We show that longer-term (5 years) experimental winter warming at the same site altered microbial communities (p < 0.040). Thaw depth correlated the strongest with community assembly and interaction networks, implying that warming-accelerated tundra thaw fundamentally restructured the microbial communities. Both carbon decomposition and methanogenesis genes increased in relative abundance under warming, and their functional structures strongly correlated (R 2 > 0.725, p < 0.001) with ecosystem respiration or CH 4 flux., Conclusions: Our results demonstrate that microbial responses associated with carbon cycling could lead to positive feedbacks that accelerate SOC decomposition in tundra regions, which is alarming because SOC loss is unlikely to subside owing to changes in microbial community composition. Video Abstract.

Listeria monocytogenes , which causes serious foodborne infections and public health problems worldwide, is one of the most important foodborne pathogens. Linalool has been identified as an antimicrobial agent against some microorganism, but its mechanism of action is currently unclear. Here, we investigated the efficacy of linalool against L. monocytogenes while planktonic and as a biofilm and explored potential mechanisms of action. Linalool exhibited strong anti-listeria activity in the planktonic stage. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) observations revealed seven stages were classified of cells at microscopic level. Mesosome-like structures were observed for the first time in L. monocytogenes after linalool treatment. Linalool also showed significant anti-biofilm activity through both dispersal and killing of cells in the biofilm based on confocal scanning laser microscopy (CLSM) and SEM imaging, crystal violet staining, XTT and COMSTAT assays. Moreover, comparative transcriptome analysis demonstrated many potential mechanisms of action for linalool and some important pathways were screened out through the analysis of GO enrichment and KEGG. Our study provides evidence that linalool exhibits a strong antimicrobial activity against both the planktonic and biofilm forms of L. monocytogenes and gives insight into its mechanism of action., (Copyright © 2019 Gao, Van Nostrand, Zhou, Zhong, Chen and Guo.)

Electronic waste (e-waste) has caused a severe worldwide pollution problem. Despite increasing isolation of degradative microorganisms from e-waste contaminated environments, the mechanisms underlying their adaptive evolution in such habitats remain unclear. Sphingomonads generally have xenobiotic-degrading ability and may play important roles in bioremediation. Sphingobium hydrophobicum C1 T , characterized with superior cell surface hydrophobicity, was recently isolated from e-waste contaminated river sediment. To dissect the mechanisms driving its adaptive evolution, we evaluated its stress resistance, sequenced its genome and performed comparative genomic analysis with 19 other Sphingobium strains. Strain C1 T can feed on several kinds of e-waste-derived xenobiotics, exhibits a great resistance to heavy metals and possesses a high colonization ability. It harbors abundant genes involved in environmental adaptation, some of which are intrinsic prior to experiencing e-waste contamination. The extensive genomic variations between strain C1 T and other Sphingobium strains, numerous C1 T -unique genes, massive mobile elements and frequent genome rearrangements reflect a high genome plasticity. Positive selection, gene duplication, and especially horizontal gene transfer drive the adaptive evolution of strain C1 T . Moreover, presence of type IV secretion systems may allow strain C1 T to be a source of beneficial genes for surrounding microorganisms. This study provides new insights into the adaptive evolution of sphingomonads, and potentially guides bioremediation strategies., (Copyright © 2019 Song, Chen, Xu, Hai, Zhou, Tian, Van Nostrand, Kempher, Guo, Sun and Zhou.)

Trait-based ecology claims to offer a mechanistic approach for explaining the drivers that structure biological diversity and predicting the responses of species, trophic interactions and ecosystems to environmental change. However, support for this claim is lacking across broad taxonomic groups. A framework for defining ecosystem processes in terms of the functional traits of their constituent taxa across large spatial scales is needed. Here, we provide a comprehensive assessment of the linkages between climate, plant traits and soil microbial traits at many sites spanning a broad latitudinal temperature gradient from tropical to subalpine forests. Our results show that temperature drives coordinated shifts in most plant and soil bacterial traits but these relationships are not observed for most fungal traits. Shifts in plant traits are mechanistically associated with soil bacterial functional traits related to carbon (C), nitrogen (N) and phosphorus (P) cycling, indicating that microbial processes are tightly linked to variation in plant traits that influence rates of ecosystem decomposition and nutrient cycling. Our results are consistent with hypotheses that diversity gradients reflect shifts in phenotypic optima signifying local temperature adaptation mediated by soil nutrient availability and metabolism. They underscore the importance of temperature in structuring the functional diversity of plants and soil microbes in forest ecosystems and how this is coupled to biogeochemical processes via functional traits.

The biodiversity of the mycobiome, an important component of the oral microbial community, and the roles of fungal-bacterial and fungal-immune system interactions in the pathogenesis of oral lichen planus (OLP) remain largely uncharacterized. In this study, we sequenced the salivary mycobiome and bacteriome associated with OLP. First, we described the dysbiosis of the microbiome in OLP patients, which exhibits lower levels of fungi and higher levels of bacteria. Significantly higher abundances of the fungi Candida and Aspergillus in patients with reticular OLP and of Alternaria and Sclerotiniaceae&#95;unidentified in patients with erosive OLP were observed compared to the healthy controls. Aspergillus was identified as an "OLP-associated" fungus because of its detection at a higher frequency than in the healthy controls. Second, the co-occurrence patterns of the salivary mycobiome-bacteriome demonstrated negative associations between specific fungal and bacterial taxa identified in the healthy controls, which diminished in the reticular OLP group and even became positive in the erosive OLP group. Moreover, the oral cavities of OLP patients were colonized by dysbiotic oral flora with lower ecological network complexity and decreased fungal-Firmicutes and increased fungal-Bacteroidetes sub-networks. Third, several keystone fungal genera (Bovista, Erysiphe, Psathyrella, etc.) demonstrated significant correlations with clinical scores and IL-17 levels. Thus, we established that fungal dysbiosis is associated with the aggravation of OLP. Fungal dysbiosis could alter the salivary bacteriome or may reflect a direct effect of host immunity, which participates in OLP pathogenesis.

Microorganisms in wastewater treatment plants (WWTPs) are essential for water purification to protect public and environmental health. However, the diversity of microorganisms and the factors that control it are poorly understood. Using a systematic global-sampling effort, we analysed the 16S ribosomal RNA gene sequences from ~1,200 activated sludge samples taken from 269 WWTPs in 23 countries on 6 continents. Our analyses revealed that the global activated sludge bacterial communities contain ~1 billion bacterial phylotypes with a Poisson lognormal diversity distribution. Despite this high diversity, activated sludge has a small, global core bacterial community (n = 28 operational taxonomic units) that is strongly linked to activated sludge performance. Meta-analyses with global datasets associate the activated sludge microbiomes most closely to freshwater populations. In contrast to macroorganism diversity, activated sludge bacterial communities show no latitudinal gradient. Furthermore, their spatial turnover is scale-dependent and appears to be largely driven by stochastic processes (dispersal and drift), although deterministic factors (temperature and organic input) are also important. Our findings enhance our mechanistic understanding of the global diversity and biogeography of activated sludge bacterial communities within a theoretical ecology framework and have important implications for microbial ecology and wastewater treatment processes.

While functional gene arrays (FGAs) have greatly expanded our understanding of complex microbial systems, specificity, sensitivity, and quantitation challenges remain. We developed a new generation of FGA, GeoChip 5.0, using the Agilent platform. Two formats were created, a smaller format (GeoChip 5.0S), primarily covering carbon-, nitrogen-, sulfur-, and phosphorus-cycling genes and others providing ecological services, and a larger format (GeoChip 5.0M) containing the functional categories involved in biogeochemical cycling of C, N, S, and P and various metals, stress response, microbial defense, electron transport, plant growth promotion, virulence, gyrB , and fungus-, protozoan-, and virus-specific genes. GeoChip 5.0M contains 161,961 oligonucleotide probes covering >365,000 genes of 1,447 gene families from broad, functionally divergent taxonomic groups, including bacteria (2,721 genera), archaea (101 genera), fungi (297 genera), protists (219 genera), and viruses (167 genera), mainly phages. Computational and experimental evaluation indicated that designed probes were highly specific and could detect as little as 0.05 ng of pure culture DNAs within a background of 1 μg community DNA (equivalent to 0.005% of the population). Additionally, strong quantitative linear relationships were observed between signal intensity and amount of pure genomic (∼99% of probes detected; r > 0.9) or soil (∼97%; r > 0.9) DNAs. Application of the GeoChip to a contaminated groundwater microbial community indicated that environmental contaminants (primarily heavy metals) had significant impacts on the biodiversity of the communities. This is the most comprehensive FGA to date, capable of directly linking microbial genes/populations to ecosystem functions. IMPORTANCE The rapid development of metagenomic technologies, including microarrays, over the past decade has greatly expanded our understanding of complex microbial systems. However, because of the ever-expanding number of novel microbial sequences discovered each year, developing a microarray that is representative of real microbial communities, is specific and sensitive, and provides quantitative information remains a challenge. The newly developed GeoChip 5.0 is the most comprehensive microarray available to date for examining the functional capabilities of microbial communities important to biogeochemistry, ecology, environmental sciences, and human health. The GeoChip 5 is highly specific, sensitive, and quantitative based on both computational and experimental assays. Use of the array on a contaminated groundwater sample provided novel insights on the impacts of environmental contaminants on groundwater microbial communities., (Copyright © 2019 Shi et al.)

The effective utilization of slag-based Silicon fertilizer (silicate fertilizer) in agriculture to improve crop productivity and to mitigate environmental consequences turns it into a high value added product in sustainable agriculture. Despite the integral role of soil microbiome in agricultural production and virtually all ecosystem processes, our understanding of the microbial role in ecosystem functions and agricultural productivity in response to the silicate fertilizer amendment is, however, elusive. In this study, using 16S rRNA gene and ITS amplicon illumina sequencing and a functional gene microarray, i.e., GeoChip 5, we report for the first time the responses of soil microbes and their functions to the silicate fertilizer amendment in two different geographic races of Oryza sativa var. Japonica (Japonica rice) and var. Indica (Indica rice). The silicate fertilizer significantly increased soil pH, photosynthesis rate, nutrient (i.e., C, Si, Fe, P) availability and crop productivity, but decreased N availability and CH 4 and N 2 O emissions. Moreover, the silicate fertilizer application significantly altered soil bacterial and fungal community composition and increased abundance of functional genes involved in labile C degradation, C and N fixation, phosphorus utilization, CH 4 oxidation, and metal detoxification, whereas those involve in CH 4 production and denitrification were decreased. The changes in the taxonomic and functional structure of microbial communities by the silicate fertilizer were mostly regulated by soil pH, plant photosynthesis, and nutrient availability. This study provides novel insights into our understanding of microbial functional processes in response to the silicate fertilizer amendment in rice cropping systems and has important implications for sustainable rice production., (Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.)