Anthropogenic vs. natural habitats: Higher microbial biodiversity pays the trade-off of lower connectivity

Climate change and anthropogenic disturbances are known to influence soil biodiversity. The objectives of this study were to compare the community composition, species coexistence patterns, and ecological assembly processes of soil microbial communities in a paired setting featuring a natural and an anthropogenic ecosystem facing each other at identical climatic, pedological, and vegetational conditions. A transect gradient from forest to seashore allowed for sampling across different habitats within both sites. The field survey was carried out at two adjacent strips of land within the Po River delta lagoon system (Veneto, Italy) one of which is protected within a natural preserve and the other has been converted for decades into a tourist resort. The anthropogenic pressure interestingly led to an increase in the α-diversity of soil microbes but was accompanied by a reduction in β-diversity. The community assembly mechanisms of microbial communities differentiate in natural and anthropic ecosystems: for bacteria, in natural ecosystems deterministic variables and homogeneous selection play a main role (51.92%), while stochastic dispersal limitation (52.15%) is critical in anthropized ecosystems; for fungi, stochastic dispersal limitation increases from 38.1% to 66.09% passing from natural to anthropized ecosystems. We are on calcareous sandy soils and in more natural ecosystems a variation of topsoil pH favors the deterministic selection of bacterial communities, while a divergence of K availability favors stochastic selection. In more anthropized ecosystems, the deterministic variable selection is influenced by the values of SOC. Microbial networks in the natural system exhibited higher numbers of nodes and network edges, as well as higher averages of path length, weighted degree, clustering coefficient, and density than its equivalent sites in the more anthropically impacted environment. The latter on the other hand presented a stronger modularity. Although the influence of stochastic processes increases in anthropized habitats, niche-based selection also proves to impose constraints on communities. Overall, the functionality of the relationships between groups of microorganisms co-existing in communities appeared more relevant to the concept of functional biodiversity in comparison to the plain number of their different taxa. Fewer but functionally more organized lineages displayed traits underscoring a better use of the resources than higher absolute numbers of taxa when those are not equally interconnected in their habitat exploitation. However, considering that network complexity can have important implications for microbial stability and ecosystem multifunctionality, the extinction of complex ecological interactions in anthropogenic habitats may impair important ecosystem services that soils provide us.

Co-occurrence patterns of gut microbiome, antibiotic resistome and the perturbation of dietary uptake in captive giant pandas

The microbiome is a key source of antibiotic resistance genes (ARGs), significantly influenced by diet, which highlights the interconnectedness between diet, gut microbiome, and ARGs. Currently, our understanding is limited on the co-occurrence among gut microbiome, antibiotic resistome in the captive giant panda and the perturbation of dietary uptake, especially for the composition and forms in dietary nutrition. Here, a qPCR array with 384 primer sets and 16 S rRNA gene amplicon sequencing were used to characterize the antibiotic resistome and microbiomes in panda feces, dietary bamboo, and soil around the habitat. Diet nutrients containing organic and mineral substances in soluble and insoluble forms were also quantified. Organic and mineral components in water-unextractable fractions were 7.5 to 139 and 637 to 8695 times higher than those in water-extractable portions in bamboo and feces, respectively, while the latter contributed more to the variation (67.5 %) of gut microbiota. Streptococcus, Prevotellaceae, and Bacteroides were the dominant genera in giant pandas. The ARG patterns in panda guts showed higher diversity in old individuals but higher abundance in young ones, driven directly by the bacterial community change and mobile genetic element mediation and indirectly by dietary intervention. Our results suggest that dietary nutrition mainly accounts for the shift of gut microbiota, while bacterial community and mobile genetic elements influenced the variation of gut antibiotic resistome.

Differences of bacterioplankton communities between the source and upstream regions of the Yangtze River: microbial structure, co-occurrence pattern, and environmental influencing factors

The source area of the Yangtze River is located in the hinterland of the Qinghai-Tibet Plateau, which is known as the "Earth's third pole." It is the water conservation area and the natural barrier of the ecosystem of the Yangtze River basin. It is also the most sensitive area of the natural ecosystem, and the ecological environment is very fragile. Microorganisms play key roles in the biogeochemical processes of water. In this paper, the bacterioplankton communities in the source and upstream regions of the Yangtze River were studied based on 16S rRNA high-throughput sequencing, and their environmental influencing factors were further analyzed. Results showed that the upstream region had higher richness and diversity than the source region. The predominant bacterial phyla in the source and upstream regions were Proteobacteria, Firmicutes, and Actinobacteriota. The bacterial phyla associated with municipal pollution and opportunistic pathogen, such as Firmicutes and Actinobacteriota, were more abundant in the upstream. By contrast, distinct planktonic bacterial genera associated with mining pollution, such as Acidiphilium and Acidithiobacillus, were more abundant in the source region. The co-occurrence network showed that the interaction of bacterioplankton community is more frequent in the upstream. The bacterioplankton community compositions, richness, and functional profiles were affected by the spatial heterogeneity. Moreover, variation partitioning analysis further confirmed that the amount of variation in the source region independently explained by variables of altitude was the largest, followed by water nutrient. This paper revealed the spatial distribution of planktonic bacterial communities in the source and upstream regions of the Yangtze River and its correlation with environmental factors, providing information support for ensuring the health and safety of aquatic ecosystems in the Yangtze River Basin.

Impacts and mechanism of coal fly ash on kitchen waste composting performance: The perspective of microbial community

Aerobic composting is eco-friendly and sustainable practice for kitchen waste (KW) disposal to restore soil fertility and reduce environmental risks. However, KW compact structure, perishable nature, acidification by anaerobic acidogens, inhibits the metabolism of aerobic microbes, insufficient breakdown of organic matters, and prolong the composting duration. This study, co-composted coal fly ash (FA), to regulate bacterial dynamics, co-occurrence patterns and nutrients transformation in KW composting. Our results indicated, FA created suitable environment by increasing pH and temperature, which facilitated the proliferation and reshaping of microbial community. FA fostered the relative abundances of phlya (Proteobacteria, Chloroflexi and Actinobacteriota) and genera (Bacillus, Paenibacillus and Lysinibacillus), which promoted the nutrients transformation (phosphorus and nitrogen) in KW compost. FA enhanced the mutualistic correlations between bacterial communities, promoted the network complexity (nodes & edges) and contains more positive connections, which reflect the FA amendment effects. KW mature compost seed germination index reached >85% of FA treatment, indicated the final products fully met the Chinese national standard for organic fertilizer. These findings might provide opportunity to advance the KW composting and collaborative management of multiple waste to curb the current environmental challenges.

Distinctive species interaction patterns under high nitrite stress shape inefficient denitrifying phosphorus removal performance

Denitrifying phosphorus removal using nitrite as an electron acceptor is an innovative, resource-efficient approach for nitrogen and phosphorus removal. However, the inhibitory effects of nitrite on anoxic phosphorus uptake and process stability are unclear. This study investigated the total phosphorus removal performance under nitrite stress and analyzed microbiome responses in 186 sludge samples. The results indicated that the total phosphorus removal rates and dominant taxon abundance were highly similar under nitrite stress. High nitrite stress induced a community-state shift, leading to unstable dynamics and decreased total phosphorus removal. This shift resulted from increased species cooperation. Notably, the shared genera OLB8 and Zoogloea under non-inhibitory nitrite stress, suggesting their vital roles in mitigating nitrite stress by enhancing carbon and energy metabolism. The response patterns of these bacterial communities to high nitrite stress can guide the design and optimization of high-nitrogen wastewater reactors.

Hydrological disturbances enhance stochastic assembly processes and decrease network stability of algae communities in a highland floodplain system

Floodplains are hotspots for biodiversity research and conservation worldwide. Hydrological disturbances can profoundly influence the ecological processes and functions of floodplain systems by altering key biological groups such as algae communities. However, the impacts of flood disturbance on the assembly processes and co-occurrence patterns of algae communities in floodplain ecosystems are still unclear. To ascertain the response patterns of algae communities to flood disturbance, we characterized planktonic and benthic algae communities in 144 water and sediment samples collected from the Tibetan floodplain during non-flood and flood periods based on 23S ribosomal RNA gene sequencing. Results showed that planktonic algae exhibited higher diversity and greater compositional variations compared with benthic communities after flood disturbance. Flooding promoted algae community homogenization at horizontal (rivers vs. oxbow lakes) and vertical levels (water vs. sediment). Stochastic processes governed the assembly of distinct algae communities, and their ecological impacts were enhanced in response to flooding. In the non-flood period, dispersal limitation (81.78 %) was the primary ecological process driving algae community assembly. In the flood period, the relative contribution of ecological drift (72.91 %) to algae community assembly markedly increased, with dispersal limitation (22.61 %) being less important. Flooding reduced the interactions among algae taxa, resulting in lower network complexity and stability. Compared with the planktonic algae subnetworks, the benthic subnetworks showed greater stability in the face of flooding. Findings of this study broaden our understanding of how algae communities respond to hydrological disturbances from an ecological perspective and could be useful for the management of highland floodplain ecosystems.

Core community drives phyllosphere bacterial diversity and function in multiple ecosystems

The phyllosphere provides a habitat for a large sum of microorganisms which are modulated by numerous biotic and abiotic factors. While it is logical that host lineage must have some effect on the phyllosphere habitat, it is unclear if phyllospheres harbor similar microbial core communities across multiple ecosystems at the continental-scale. Here we collected 287 phyllosphere bacterial communities from seven ecosystems (including paddy field, dryland, urban area, protected agricultural land, forest, wetland, and grassland) in east-China to identify the regional core community and to characterize the importance of such communities in maintaining phyllosphere bacterial community structure and function. Despite significantly different bacterial richness and structure, the seven studied ecosystems contained a similar regional core community of 29 OTUs that comprised 44.9 % of the total bacterial abundance. The regional core community was less affected by environmental variables and less connected in the co-occurrence network compared with other non-core OTUs (the whole minus regional core community). Furthermore, the regional core community also had a large proportion (>50 %) of a constrained set of nutrient metabolism related functional potentials and less functional redundancy. This study suggests there is a robust regional core phyllosphere community regardless of ecosystem or spatial and environmental heterogeneity, and supports the argument that core communities are pivotal in maintaining microbial community structure and function.

Unveiling the impact and mechanisms of Cd-driven ecological assembly and coexistence of bacterial communities in coastal sediments of Yellow Sea

The microbial community assembly processes and underlying mechanisms in response to heavy metal accumulation in coastal sediments remain underexplored. In this study, the heavy metal concentration in samples were found below the marine sediment quality standards. Through partial Mantel tests and linear regression analysis, Cd was identified as the major influencing factor, displaying strongest correlation with the bacterial community in the sediments. The class Desulfuromonadia was identified as a biomarker which showed enrichment in the sediments with high Cd content. Additionally, the results of null model and the neutral community model demonstrated the prominent role of stochastic processes in the assembly of bacterial community. However, with the increase in Cd concentration, the influence of selection processes intensified, resulting in a decline in species migration rate and subsequent reduction in ecological niche width. Furthermore, the intensified competition and an increase in keystone species among bacterial populations further enhanced the stability of the microbial co-occurrence network in response to high Cd concentration. This study offers an insight into the effects of heavy metal on microbial assembly and coexistence, which are conducive to marine ecosystem management and conservation.

Copper and cadmium co-contamination affects soil bacterial taxonomic and functional attributes in paddy soils

Microorganisms inhabiting heavy metal-contaminated soils have evolved specific metabolic capabilities to survive, which has the potential for effective bioremediation. However, the ecological consequence of copper (Cu) and cadmium (Cd) on bacterial taxonomic and functional attributes of rice field remains unclear. Here, we selected paddy soils along a polluted river in southern China to evaluate the role of Cu and Cd contaminant fractions in regulating bacterial co-occurrence patterns. We also assessed the effects of these heavy metal fractions on the relative abundance of functional genes using shotgun metagenomic analysis. Soil Cu and Cd concentrations in paddy soils gradually decreased from upstream to downstream of the river, and had a greater impact on bacterial communities and metabolic potentials than soil general properties. Soil Cu and Cd contamination led to drastic changes in the cumulative relative abundance of ecological modules in bacterial co-occurrence networks. Bacteria associated with AD3, HSB_OF53-F07 (both belonging to Chloroflexi), Rokubacteriales, and Nitrospira were identified as tolerant to Cu and Cd contamination. The Cu and Cd contaminant fractions were positively correlated with the genes involved in metal resistance, carbon (C) fixation, nitrification, and denitrification, but negatively correlated with the genes related to nitrogen (N) fixation. These results indicated that soil Cu and Cd pollution not only enriched metal resistant genes, but also affected genes related to microbial C and N cycling. This is critical for facilitating microbiome bioremediation of metal-contaminated paddy soils.

Conservation tillage increases surface soil organic carbon stock by altering fungal communities and enzyme activity

Fungal communities play a key role in the decomposition of crop residues and affect soil organic carbon (SOC) dynamics. Conservation tillage enhances SOC sequestration and mitigate global climate change. However, the impact of long-term tillage practices on fungal community diversity and its relation to SOC stock remains unclear. The objectives of this study were to evaluate the relationship between extracellular enzyme activities and fungal community diversity and SOC stock under different tillage practices. A field experiment was conducted with four tillage practices: (i) no-tillage with straw removal (NT0), (ii) no-tillage with straw retention (NTSR, conservation tillage), (iii) plough tillage with straw retention (PTSR), and (iv) rotary tillage with straw retention (RTSR). The results showed that the SOC stock in NTSR was higher than other treatments in the 0-10 cm soil layer. Compared to NT0, NTSR significantly increased soil β-glucosidase, xylosidase, cellobiohydrolase, and chitinase activities at 0-10 cm soil depth (P < 0.05). However, different tillage methods with straw returning had no significant effects on enzyme activity at 0-10 cm soil depth. The observed species and Chao1 index of the fungal communities under NTSR were 22.8% and 32.1% lower than under RTSR in the 0-10 cm soil layer, respectively. The composition, structure, and co-occurrence network of fungal communities differed across tillage practices. A partial least squares path model (PLS-PM) analysis indicated that C-related enzymes were the most influential factors associated with SOC stock. Soil physicochemical properties and fungal communities affected extracellular enzyme activities. Overall, conservation tillage can promote surface SOC stock, which was associated with increased enzyme activity.

Assembly processes of bacterial and fungal communities in metal(loid)s smelter soil

There are few studies on concurrent bacterial and fungal community assembly processes that govern the metal(loid)s biogeochemical cycles at smelters. Here, a systematic investigation combined geochemical characterization, co-occurrence patterns, and assembly mechanisms of bacterial and fungal communities inhabiting soils around an abandoned arsenic smelter. Acidobacteriota, Actinobacteriota, Chloroflexi, and Pseudomonadota were dominant in bacterial communities, whereas Ascomycota and Basidiomycota dominated fungal communities. The random forest model indicated the bioavailable fractions of Fe (9.58%) were the main positive factor driving the beta diversity of bacterial communities, and the total N (8.09%) was the main negative factor for fungal communities. Microbe-contaminant interactions demonstrate the positive impact of the bioavailable fractions of certain metal(loid)s on bacteria (Comamonadaceae and Rhodocyclaceae) and fungi (Meruliaceae and Pleosporaceae). The fungal co-occurrence networks exhibited more connectivity and complexity than the bacterial networks. The keystone taxa were identified in bacterial (including Diplorickettsiaceae, norank_o_Candidatus_Woesebacteria, norank_o_norank_c_AT-s3-28, norank_o_norank_c_bacteriap25, and Phycisphaeraceae) and fungal (including Biatriosporaceae, Ganodermataceae, Peniophoraceae, Phaeosphaeriaceae, Polyporaceae, Teichosporaceae, Trichomeriaceae, Wrightoporiaceae, and Xylariaceae) communities. Meanwhile, community assembly analysis revealed that deterministic processes dominated the microbial community assemblies, which were highly impacted by pH, total N, and total and bioavailable metal(loid) content. This study provides helpful information to develop bioremediation strategies for the mitigation of metal(loid)s-polluted soils.

Heavy metal contamination affects the core microbiome and assembly processes in metal mine soils across Eastern China

Mining activities in metal mine areas cause serious environmental pollution, thereby imposing stresses to soil ecosystems. Investigating the ecological pattern underlying contaminated soil microbial diversity is essential to understand ecosystem responses to environment changes. Here we collected 624 soil samples from 49 representative metal mines across eastern China and analyzed their soil microbial diversity and biogeographic patterns by using 16 S rRNA gene amplicons. The results showed that deterministic factors dominated in regulating the microbial community in non-contaminated and contaminated soils. Soil pH played a key role in climatic influences on the heavy metal-contaminated soil microbial community. A core microbiome consisting of 25 taxa, which could be employed for the restoration of contaminated soils, was identified. Unlike the non-contaminated soil, stochastic processes were important in shaping the heavy metal-contaminated soil microbial community. The largest source of variations in the soil microbial community was land use type. This result suggests that varied specific ecological remediation strategy ought to be developed for differed land use types. These findings will enhance our understanding of the microbial responses to anthropogenically induced environmental changes and will further help to improve the practices of soil heavy metal contamination remediation.

Responses of abundant and rare prokaryotic taxa in a controlled organic contaminated site subjected to vertical pollution-induced disturbances

Soil microbiota as the key role mediates the natural attenuation process of organic contaminated sites, and therefore illuminating the mechanisms underlying the responses of abundant and rare species is essential for understanding ecological processes, maintaining ecosystem stability, and regulating natural attenuation well. Here, we explored the distributional characteristics, ecological diversities, and co-occurrence patterns of abundant and rare prokaryotic subcommunities using 16S rRNA high-throughput sequencing in vertical soil profiles of a controlled organic contaminated site. Results showed that abundant prokaryotic taxa were widespread across all soil samples, whereas rare counterparts were unbalancedly distributed. Rare subcommunity had more taxonomic groups and higher α- and β-diversities than abundant subcommunity. Both of these two subcommunities surviving in the organic polluted site possessed the potential of degrading organic contaminants. Abundant subcommunity was little affected by abiotic factors and mainly shaped by soil depth, while rare one was sensitive to environmental disturbances and presented a non-depth-dependent structure. Co-occurrence analysis revealed that rare taxa were more situated at the center of the network and more inclined to cooperate with non-abundant species than abundant taxa, which might play crucial roles in enhancing the resilience and resistance of prokaryotic community and maintaining its structure and stability. Overall, our results suggest that abundant and rare prokaryotic subcommunities present different responses to physicochemical factors and pollution characteristics along vertical soil profiles of organic contaminated sites undergoing natural attenuation.

particle-attached bacterial communities across different habitats and seasons in shallow, eutrophic Lake Taihu

Eutrophication due to nitrogen and phosphorus input is an increasing problem in lake ecosystems. Free-living (FL) and particle-attached (PA) bacterial communities play a primary role in mediating biogeochemical processes in these lakes and in responding to eutrophication. However, knowledge of factors governing function, assembly mechanisms, and co-occurrence patterns of these communities remain poorly understood and are key challenges in microbial ecology. To address this knowledge gap, we collected 96 samples from Lake Taihu across four seasons and investigated the bacterial community using 16S rRNA gene sequencing. Our results demonstrate that the α-diversity, β-diversity, community composition, and functional composition of FL and PA bacterial communities exhibited differing spatiotemporal dynamics. FL and PA bacterial communities displayed similar distance-decay relationships across seasons. Deterministic processes (i.e., environmental filtering and species interaction) were the primary factors shaping community assembly in both FL and PA bacteria. Similar environmental factors shaped bacterial community structure while different environmental factors drove bacterial functional composition. Habitat filtering influenced enrichment of bacteria within specific functional groups. Among them, the FL bacterial community appeared to play a critical role in methane-utilization, whereas the PA bacteria contributed more to biogeochemical cycling of carbon. FL and PA bacterial communities exhibited distinct co-occurrence pattern across different seasons. In the FL network, Methylotenera and Methylophilaceae were identified as keystone taxa, while Burkholderiaceae and the hgcI clade were keystone taxa in the PA network. The PA bacterial community appeared to possess greater stability in the face of environmental change than did FL counterparts. These results broaden our knowledge of the driving factors, co-occurrence patterns, and assembly processes in FL and PA bacterial communities in eutrophic ecosystems and provide improved insight into the underlying mechanisms responsible for these results.

Fecal microbiota dynamics and its relationship to diarrhea and health in dairy calves

BACKGROUND

Diarrhea is a major cause of morbidity and mortality in young calves, resulting in considerable economic loss for dairy farms. To determine if some gut microbes might have resistance to dysbiotic process with calf diarrhea by dictating the microbial co-occurrence patterns from birth to post-weaning, we examined the dynamic development of the gut microbiota and diarrhea status using two animal trials, with the first trial having 14 Holstein dairy calves whose fecal samples were collected 18 times over 78 d from birth to 15 d post-weaning and the second trial having 43 Holstein dairy calves whose fecal samples were collected daily from 8 to 18 days of age corresponding to the first diarrhea peak of trial 1.

RESULTS

Metataxonomic analysis of the fecal microbiota showed that the development of gut microbiota had three age periods with birth and weaning as the separatrices. Two diarrhea peaks were observed during the transition of the three age periods. Fusobacteriaceae was identified as a diarrhea-associated taxon both in the early stage and during weaning, and Clostridium_sensu_stricto_1 was another increased genus among diarrheic calves in the early stage. In the neonatal calves, Prevotella_2 (ASV4 and ASV26), Prevotella_9 (ASV43), and Alloprevotella (ASV14) were negatively associated with Clostridium_sensu_stricto_1 (ASV48), the keystone taxa of the diarrhea-phase module. During weaning, unclassified Muribaculaceae (ASV28 and ASV44), UBA1819 (ASV151), Barnesiella (ASV497), and Ruminococcaceae_UCG-005 (ASV254) were identified being associated with non-diarrheic status, and they aggregated in the non-diarrhea module of co-occurrence patterns wherein unclassified Muribaculaceae (ASV28) and Barnesiella (ASV497) had a direct negative relationship with the members of the diarrhea module.

CONCLUSIONS

Taken together, our results suggest that the dynamic successions of calf gut microbiota and the interactions among some bacteria could influence calf diarrhea, and some species of Prevotella might be the core microbiota in both neonatal and weaning calves, while species of Muribaculaceae might be the core microbiota in weaning calves for preventing calf diarrhea. Some ASVs affiliated with Prevotella_2 (ASV4 and ASV26), Prevotella_9 (ASV43), Alloprevotella (AVS14), unclassified Muribaculaceae (ASV28 and ASV44), UBA1819 (ASV151), Ruminococcaceae_UCG-005 (ASV254), and Barnesiella (ASV497) might be proper probiotics for preventing calf diarrhea whereas Clostridium_sensu_stricto_1 (ASV48) might be the biomarker for diarrhea risk in specific commercial farms.

Deep mining decreases the microbial taxonomic and functional diversity of subsurface oil reservoirs

Microbes in subsurface oil reservoirs play important roles in elemental cycles and biogeochemical processes. However, the community assembly pattern of indigenous microbiome and their succession under long-term human activity remain poorly understood. Here we studied the microbial community assembly in underground sandstone cores from 190 to 2050 m in northeast China and their response to long-term oil recovery (10-50 years). Indigenous microbiome in subsurface petroleum reservoirs were dominated by Gammaproteobacteria, Firmicutes, Alphaproteobacteria, Bacteroidetes, and Actinobacteria, which exhibited a higher contribution of homogenizing dispersal assembly and different taxonomy distinct ecological modules when compared with perturbed samples. Specifically, the long-term oil recovery reduced the bacterial taxonomic- and functional-diversity, and increased the community co-occurrence associations in subsurface oil reservoirs. Moreover, distinguished from the perturbed samples, both variation partition analysis and structural equation model revealed that the contents of quartz, NO₃^- and Cl^- significantly structured the α- and β-diversity in indigenous subsurface bacterial communities. These findings first provide the holistic picture of microbiome in the deep oil reservoirs, which demonstrate the significant impact of human activity on microbiome in deep continental subsurface.

Storage tank as a pretreatment unit for rainwater cleaner production: Role of biofilm bacterial communities and functional genera in water quality improvement

This study investigated the water purification function and mechanism of biofilm in storage tank, with a view to using it as a pretreatment unit for rainwater cleaner production. Shortening the hydraulic retention time (HRT) of storage tank from 12 to 4 h improved the pollutants removal performance and reduced the suspended bacteria counts. The accumulation of abundant taxa and succession of rare taxa were observed with biofilm development. Positive correlations within and across different bacterial taxa were dominant in the network, and some rare genera (Ralstonia and Micropruina) were identified as hub bacteria. Candidatus Nitrospira nitrosa and Nitrospira sp. ENR4 were two identified complete ammonia oxidizers. Denitrifying bacteria tended to enrich and formed more complex interactions over time. The main nitrogen metabolism pathways may be ammonia assimilatory, complete denitrification and dissimilatory/assimilatory nitrate reduction. HRT was negatively correlated with most dominant genera, and contributed 20.35% to the variation of functional taxa. This study highlights the self-purification function and micro-ecology of storage tank, and provides a new insight for its role in rainwater cleaner production process.

Disentangling the distinct mechanisms shaping the subsurface oil reservoir bacterial and archaeal communities across northern China

Microbes in surface ecosystem exhibit strong biogeographic patterns, and are less apparent after human management. However, in contrast with the considerable knowledge on the surface ecosystem, the microbial biogeographic patterns in deep subsurface ecosystem under artificial disturbance is poorly understood. Here, we explored the spatial scale-dependence patterns of bacterial and archaeal communities in oil reservoirs under different artificial flooding duration and environmental conditions across northern China. Bacterial and archaeal communities of oil reservoirs exhibited distinct assembly patterns with a stronger distance-decay relationship in archaeal communities than bacterial communities, as different environmental factors linked to the diversity of bacteria and archaea. Specifically, bacterial and archaeal network properties revealed a significant correlation with spatial reservoir isolation by distinct co-occurrence patterns. The co-occurrences of bacterial communities were more complex in high temperature and alkaline pH, while archaeal co-occurrences were more frequent in low temperature and neutral pH. Potential functions in bacterial communities were more connected with chemoheterotrophy, whereas methanogenesis was abundant in archaeal communities, as confirmed by both keystone taxa and main ecological clusters in networks. This revealed that different mechanisms underlain geography and co-occurrence patterns of bacteria and archaea in oil reservoirs, providing a new insight for understanding biogeography and coexistence theory in deep subsurface ecosystem.

Succession of diazotroph community and functional gene response to inoculating swine manure compost with a lignocellulose-degrading consortium

Diazotroph community contributes to the nitrogen mass and improves the agronomic quality of composting product, but their responses to microbial inoculation during composting are unclear. In this study, the lignocellulose-degrading consortium was inoculated at different levels (0%: CK (control) and 10%: T) to investigate their effects on the variations in the diazotroph community and functional gene during composting. In the later composting phase, the nifH gene copy number was 17.50-25.28% higher in T than CK. The nitrogenase abundance in CK and T were 0.042% and 0.046% in composting product, respectively. Network analysis indicated that inoculation affected the co-occurrence patterns of the diazotroph community and changed the keystone species composition. Partial least-squares path modeling showed that available carbon sources and the succession of the diazotroph community mainly determined the increased abundance of nifH gene. Microbial inoculation stimulated the diazotrophs activities, and was conducive to the nitrogen production in composting product.

Behavior of antibiotic resistance genes in a wastewater treatment plant with different upgrading processes

Wastewater treatment plants (WWTPs) in China have been upgraded or renovated with a variety of emerging processes, but a comprehensive understanding of the behavior of antibiotic resistance genes (ARGs) in these WWTPs is still lacking. Here, the distribution of ARGs and bacterial community were investigated in a wastewater treatment plant with upgrading processes (WWTP-UP). 238 unique ARGs were detected in all samples. During the study period, the average ARGs concentration decreased by 98.4% along the entire treatment process. The removal efficiency of A²/O-membrane bioreactor (MBR) process was significantly higher than that of A²/O-high efficiency flocculent settling/cloth media filter (HEFS/CMF) process (p < 0.05), which corresponded to 3.5 and 2.1 log values on average, respectively. Notably, 35 ARGs and 14 mobile genetic elements (MGEs) were persistent in all samples. Based on the co-occurrence pattern revealed by network analysis, persistent ARGs possibly spread through the transfer of persistent MGEs among persistent bacteria. Using multiple linear regression analysis, we obtained 3 to 5 possible indicators for major ARG types, which might be served to evaluate the general distribution of ARGs or even predict the abundance of different ARG types. Our findings provide new insights into the impacts of upgrading process on ARGs and highlight the need for better strategies to improve ARGs elimination in WWTPs.

Floral fungal-bacterial community structure and co-occurrence patterns in four sympatric island plant species

Flowers' fungal and bacterial communities can exert great impacts on host plant wellness and reproductive success-both directly and indirectly through species interactions. However, information about community structure and co-occurrence patterns in floral microbiome remains scarce. Here, using culture-independent methods, we investigated fungal and bacterial communities associated with stamens and pistils of four plant species (Scaevola taccada, Ipomoea cairica, Ipomoea pes-caprae, and Mussaenda kwangtungensis) growing together under the same environment conditions in an island located in South China. Plant species identity significantly influenced community composition of floral fungi but not bacteria. Stamen and pistil microbiomes did not differ in community composition, but differed in co-occurrence network topological features. Compared with the stamen network, pistil counterpart had fewer links between bacteria and fungi and showed more modular but less concentrated and connected structure. In addition, degree distribution of microbial network in each host species and each microhabitat (stamen or pistil) followed a significant power-law pattern. These results enhance our understanding in the assembly principles and ecological interactions of floral microbial communities.

Roles of nxrA-like oxidizers and nirS-like reducers in nitrite conversion during swine manure composting

Nitrite has a key role in nitrogen conversion during composting. In this study, the dynamic changes in the NO₂^- contents, abundances of nirS and nxrA, and the bacteria that harbored these genes were determined during composting. NO₂^- accumulated during the initial composting stage. The nirS gene was abundant throughout composting, whereas the nxrA gene was only abundant in the late composting phases. Ralstonia sp. and Thauera sp. were the dominant denitrifiers that harbored nirS, and Nitrobacter winogradskyi Nb-255 was the dominant nitrifier that harbored nxrA. Structural equation modeling showed that NO₂^- was mainly reduced by nirS in the early phases, and oxidized by nxrA in the late phases, but especially in the maturity phase. Network analysis showed that the dominant bacteria harboring nirS and nxrA were hubs in the modules related to the reduction and oxidation of NO₂^-, and they had competitive relationships during the cooling and maturity phases.

Effects of inoculating with lignocellulose-degrading consortium on cellulose-degrading genes and fungal community during co-composting of spent mushroom substrate with swine manure

Composting is used widely for recycling spent mushroom substrate (SMS). This study investigated the effects of inoculating a lignocellulose-degrading consortium at two levels comprising 0% (control: CK) and 10% (T) on the fungal community and cellulose-degrading genes during SMS co-composting with swine manure. Lignocellulose degradation rate in T was 8.77-34.45% higher compared with CK. Inoculation affected the distribution of the fungal community, increased the community diversity, and inhibited pathogens. Network analysis showed that inoculation changed the co-occurrence patterns of the fungal communities and made the co-composting system more stable. The relative abundances of glycoside hydrolase genes GH3E (fungal GH3), GH6, and GH7 were 0.45, 0.09, and 0.39 logs higher in T, respectively, than CK. Partial least-squares path modeling suggested that the variations in cellulose-degrading genes were driven mainly by changes in the fungal community during co-composting. Therefore, the lignocellulose-degrading consortium accelerated the transformation of lignocellulose to facilitate safer composting.

Divergent responses of bacterial activity, structure, and co-occurrence patterns to long-term unbalanced fertilization without nitrogen, phosphorus, or potassium in a cultivated vertisol

Unbalanced fertilization lacking nitrogen (N), phosphorus (P), or potassium (K) is a worldwide phenomenon; however, whether they affect bacterial community composition and intraspecific interactions in a similar pattern and how they affect bacterial activity are not systematically compared. Soils under different kinds of unbalanced fertilization in a 21-year field experiment were collected to investigate the variation in dehydrogenase activity (DHA), bacterial community diversity, structure, composition, and possible interactions. Compared to the balanced fertilization of NPK, the DHA from unbalanced fertilization of NP, PK, and NK was 8.70, 11.59, and 14.17% lower, respectively, and from the unfertilized treatment (Nil) was 13.41% lower; however, the Shannon index from NP, PK, and Nil was 4.48-7.21% higher and from NK was 3.95% lower. Based on principal coordinate analyses (PCoA), bacterial community structure was separated by N application or not along PCo1 and was further separated by P application or not along PCo2, indicating a more influence by N deficiency. Moreover, the structure was mainly determined by soil pH, soil organic carbon (SOC), and total phosphorus (TP). The network complexity using co-occurrence analysis followed the order NP > NPK > PK > NK > Nil, indicating a more influence by P deficiency on intraspecific interactions. Structural equation modeling (SEM) revealed that the reduced DHA in NP was mainly regulated by the decreased SOC and increased Shannon index, in PK by the decreased SOC and increased Shannon index and pH, and in NK by the decreased SOC and TP and increased PCo2. The significantly lower abundance of Bacteroidetes and Chitinophagaceae in NK may also contribute to the reduced DHA. Our results imply that N deficiency had the greatest impact on bacterial community structure and composition, P deficiency had the greatest impact on network construction and bacterial activity, and K deficiency has minimal effect. Our results also suggest that main factors regulating the variation in soil functions may vary among different nutrient deficiencies.

Variations in the denitrifying microbial community and functional genes during mesophilic and thermophilic anaerobic digestion of cattle manure

In this study, the anaerobic digestion (AD) of cattle manure was conducted at two temperatures (mesophilic: 35 °C; thermophilic: 55 °C) to analyze the dynamics of the denitrifying functional microbial community and functional genes. The cumulative N₂O production under thermophilic conditions was 130.3% higher than that under mesophilic conditions. Thermophilic AD decreased the abundance of nosZ, which was more functional than other denitrifying genes. Firmicutes, Proteobacteria, and Bacteroidetes were the main phyla, and they were also related to denitrification during AD. Redundancy analysis indicated that pH, temperature, and NH₄⁺-N mainly affected the functional bacterial community. Temperature altered the co-occurrence patterns of the bacterial community and the keystone genera in AD. Desulfovibrio in mesophilic AD and Thiobacillus in thermophilic AD were closely related to nitrogen transformation among the keystone genera. The variations in the abundances of members of the denitrifying microbial community and functional genes during AD suggest that thermophilic AD may have caused greater nitrogen losses.

Impact of copper on the diazotroph abundance and community composition during swine manure composting

Biological nitrogen fixation is a major pathway in ecosystems. This study investigated the effects of adding Cu at different levels (0, 200, and 2000 mg kg^-1) on the diazotroph community during swine manure composting. Quantitative PCR and high-throughput sequencing were used to analyze the abundances of diazotrophs and the community composition based on the nifH gene. The nifH gene copy number was relatively high in the early stage of composting and Cu had a significant inhibitory effect on the nifH copy number. Furthermore, Cu decreased the diversity of nifH and changed the microbial community structure in the early stage. The nifH genes from members of Firmicutes and Clostridium were most abundant. Co-occurrence ecological network analysis showed that the Cu treatments affected the co-occurrence patterns of diazotroph communities and reduced the associations between different diazotrophs. Interestingly, Cu may weaken symbiotic diazotrophic interactions and enhance the roles of free-living diazotrophs.

The core populations and co-occurrence patterns of prokaryotic communities in household biogas digesters

BACKGROUND

Household biogas digesters are widely used to harvest energy in rural areas of developing countries. Understanding core prokaryotic communities, their co-occurrence patterns, and their relationships to environmental factors is important to manage these small-scale anaerobic digestion systems effectively. In this study, 43 household biogas digesters were collected across eight provinces in China. Prokaryotic communities were investigated using 454 pyrosequencing of 16S rRNA genes.

RESULTS

Fourteen core genera and ten core OTUs were identified in household biogas digesters. They were mainly affiliated with the phylum Firmicutes, Synergistetes, Actinobacteria, Chloroflexi, and Spirochaetes. Core prokaryotic genera were mainly composed of Clostridium, Clostridium XI, Syntrophomonas, Cloacibacillus, Sedimentibacter, and Turicibacter. Prokaryotic communities in the 43 samples were clearly divided into two clusters. Cluster I was dominated by Clostridium, while Cluster II was dominated by members of Spirochaetes, Bacteroidales, Clostridia, and abundant syntrophs and methanogens. NH4 (+)-N and COD contributed significantly to the assembly of the prokaryotic community in Cluster I, while NH4 (+)-N, pH, and phosphate contributed significantly to Cluster II. Correlation-based network analysis showed that the prokaryotic communities in the biogas digesters were dominated by some functional modules. Cluster I was dominated by acetotrophic methanogenic modules and the Clostridium-driven primary fermentation module, while the network of Cluster II was dominated by hydrogenotrophic and acetogenic methanogenesis modules and multi-group-driven (Spirochaetes, Bacteroidales, and Clostridia) primary fermentation modules. The network of Cluster II was more complex and functionally redundant.

CONCLUSIONS

Prokaryotic communities identified in the household biogas digesters varied significantly and were affected by environmental factors, such as NH4 (+)-N, pH, and COD. However, core prokaryotic communities existed, and most of them were also dominant populations. Cosmopolitan OTUs tended to co-occur. Prokaryotic communities in biogas digesters were well organized by some functional modules. The modular structure of the prokaryotic community, which has functional redundancy, enhances the resistance against environmental stress and maintains digestion efficiency in the anaerobic digestion process.