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Microbial communities as the most important and active component of soil play a crucial role in the geochemical cycling of toxic metal(loid)s in the Pb and Zn smelting site soils. However, the relationships between soil microbial communities and the fractions of toxic metal(loid)s and the succession of soil microbial community and functions after enrichment cultivation have rarely been analyzed. In this study, the diversity and composition of microbial communities in soils before and after enrichment cultivation were investigated by high-throughput sequencing. And the co-occurrence relationships between soil microbial community after enrichment cultivation and MRGs genes were also analyzed through the BacMet database. Results showed that the dominant genus in the soils was Lactobacillus and Stenotrophomonas. The soil microbial community exhibited a notable correlation with Cd, Pb, and As, among which Cd exerted the most profound impact. Alishewanella, Pseudomonas, Massilia and Roseibacillus were significantly correlated with the fraction of Cd. After enrichment cultivation, the number of genera decrease to 96. And the dominant genus changed to Acinetobacter, Bacillus, Comamonas, Lysobacter, and Pseudoxanthomonas. High abundance of metal resistance genes (MRGs) including zntA, fpvA, zipB, cadA, czcA, czcB, czcC, zntA, arsR, pstS and pstB was found in the microbial community after enrichment cultivation. The potential host genus for MRGs was Acinetobacter, Comamonas, Lysinibacillus, Azotobacter, Bacillus, Lysobacter, Cupriavidus, Pseudoxanthomonas, and Thermomonas. Additionally, these microbial community after enrichment cultivation possessing pathways of bacterial chemotaxis and two-component systems was enabled them to adapt to the polluted environment. These observations provided potential guidance for microbe isolation and the development of strategies for the bioremediation of toxic metal(loid)s polluted soils., 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 © 2024 Elsevier B.V. All rights reserved.)

The dynamics of aquatic microbes is of great importance for comprehending the acclimatisation and evolution of microorganisms in lake ecology. However, little is known about the adaption strategies of microbial communities in East Dongting Lake, which had special and complexity geographical characteristics. A semi-enclosed lake area (A) and a waterway connected to Yangtze River (B) both existed in the lake zone. Here, we investigated bacterial and fungal community diversity, community network and community assembly processes in sediment and water. The results indicated that the proportion of OTU numbers and their relative abundance for rare and abundant taxa were different obviously between sediment and water, but not between bacteria and fungi. However, abundant subcommunities dominated the shifts of bacterial community diversity and structure in A region, while rare subcommunities for fungal community diversity. Compared to fungal community, bacterial network was more compact and more key stones were identified as rare taxa. In addition, stochastic processes (dispersal limitation) drove the community assembly of abundant and rare subcommunities, but the effects of deterministic processes (including variable and heterogeneous selections) affected more on rare rather than abundant taxa. Partial Mantel test further indicated that the effect of environmental factors was a stronger force in shaping abundant bacterial subcommunities (TOC, NH 4 + -N, TN, and ORP) and rare fungal subcommunities (ORP). Environmental factors explained more of the variation in bacterial community structure than that in fungal community structure, although they had additional effects on fungal community diversity and community assembly. Moreover, bacterial community affected the fungal community as a biotic factor in water. This research provided new insights into better understanding of microbial communities in the complex environment of the East Dongting Lake., Competing Interests: Declarations Conflict of interest The authors have no conflict of interest to report., (© 2024. The Author(s), under exclusive licence to Microbiological Society of Korea.)

The mining and smelting site soils in South China present excessive Cd pollution. However, the transport behavior of Cd in the highly weathered acidic soil layer at the lead-zinc smelting site remains unclear. Here, under different conditions of simulated infiltration, the migration behavior of Cd 2+ in acid smelting site soils at different depths was examined. The remodeling effect of Cd 2+ migration behavior on microbial community structure and the dominant microorganisms in lead-zinc sites soils was analyzed using high-throughput sequencing of 16S rRNA gene amplicons. The results revealed a specific flow rate in the range of 0.3-0.5 mL/min that the convection and dispersion have no obvious effect on Cd 2+ migration. The variation of packing porosity could only influence the migration behavior by changing the average pore velocity, but cannot change the adsorption efficiency of soil particles. The Cd has stronger migration capacity under the reactivation of acidic seepage fluid. However, in the alkaline solution, the physical properties of soil, especially pores, intercept the Cd compounds, further affecting their migration capacity. The acid-site soil with high content of SOM, amorphous Fe oxides, crystalline Fe/Mn/Al oxides, goethite, and hematite has stronger ability to adsorb and retain Cd 2+ . However, higher content of kaolinite in acidic soil will increase the potential migration of Cd 2+ . Besides, the migration behavior of Cd 2+ results in simplified soil microbial communities. Under Cd stress, Cd-tolerant genera (Bacteroides, Sphingomonas, Bradyrhizobium, and Corynebacterium) and bacteria with both acid-Cd tolerance (WCHB 1-84) were distinguished. The Ralstonia showed a high enrichment degree in alkaline Cd 2+ infiltration solution (pH 10.0). Compared to the influence of Cd 2+ stress, soil pH had a stronger ability to shape the microbial community in the soil during the process of Cd 2+ migration., (© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

High material cost is the biggest barrier for the industrial use of low-molecular-weight organics (i.e. lactate) as external carbon and electron source for sulfidogenic metal removal in sulfate-rich effluents. This study aims to provide mechanistic evidence from kinetics to microbiome analysis by batch modeling to support the possibility of decreasing the lactate input to achieve cost-effective application. The results showed that gradient COD/SO 4 2- ratios at a low level had promising treatment performance, reaching neutralized pH with nearly total elimination of COD (91%-99%), SO 4 2- (85%-99%), metals (80%-99%) including Cu, Zn, and Mn. First-order kinetics exhibited the best fit (R 2  = 0.81-0.98) to (bio)chemical reactions, and the simulation results revealed that higher COD/SO 4 2- accelerated the reaction rate of SO 4 2- and COD but not suitable to that of metals. On the other hand, we found that the decreasing COD/SO 4 2- ratio increased average path distance but decreased clustering coefficient and heterogeneity in microbial interaction network. Genetic prediction found that the sulfate-reduction-related functions were significantly correlated with the reaction kinetics changed with COD/SO 4 2- ratios. Our study, combining reaction kinetics with microbiome analysis, demonstrates that the use of lactate as a carbon source under low COD/SO 4 2- ratios entails significant efficiency of metal removal in sulfate-rich effluent using SRB-based technology. However, further studies should be carried out, including parameter-driven optimization and life cycle assessments are necessary, for its practical application., 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 © 2023. Published by Elsevier Ltd.)

The quality of fermented plant products is closely related to microbial metabolism. Here, the associations of bacterial communities, metabolites, and functional genes were explored using multi-omics techniques based on plant leaf fermentation systems. The results showed significant changes in the structure of the microbial community, with a significant decrease in Firmicutes and a significant increase in Proteobacteria. In addition, the concentration of metabolites with antibacterial, antioxidant and aroma properties increased significantly, enhancing the quality of the fermented plant leaves. Integrated macrogenomic and metabolomic analyses indicated that amino acid metabolism could be key metabolic pathway affecting fermentation quality. Actinobacteria, Proteobacteria, Firmicutes were actively involved in tyrosine metabolism (ko00350) and phenylalanine metabolism (ko00360), and are presumed to be the major groups responsible for synthesizing growth and flavor compounds. This study emphasized the important role of microorganisms in the changes of metabolites during the fermentation of plant leaves., 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 © 2023. Published by Elsevier Inc.)

Viruses are widespread in various ecosystems, and they play important roles in regulating the microbial community via host-virus interactions. Recently, metagenomic studies showed that there are extremely diverse viruses in different environments from the ocean to the human gut, but the influences of viral communities on microbial communities are poorly understood, especially in extreme environments. Here, we used metagenomics to characterize microbial communities and viral communities in acid mine drainage (AMD) and evaluated how viruses shape microbial community constrained by the harsh environments. Our results showed that AMD viral communities are significantly associated with the microbial communities, and viral diversity has positive correlations with microbial diversity. Viral community explained more variations of microbial community composition than environmental factors in AMD of a polymetallic mine. Moreover, we found that viruses harboring adaptive genes regulate a relative abundance of hosts under the modulation of environmental factors, such as pH. We also observed that viral diversity has significant correlations with the global properties of microbial cooccurrence networks, such as modularity. In addition, the results of null modeling analyses revealed that viruses significantly affect microbial community phylogeny and play important roles in regulating ecological processes of community assembly, such as dispersal limitation and homogenous dispersal. Together, these results revealed that AMD viruses are critical forces driving microbial network and community assembly via host-virus interactions. IMPORTANCE Viruses as mobile genetic elements play critical roles in the adaptive evolution of their hosts in extreme environments. However, how viruses further influence microbial community structure and assembly is still unclear. A recent metagenomic study observed diverse viruses unexplored in acid mine drainage, revealing the associations between the viral community and environmental factors. Here, we showed that viruses together with environmental factors can constrain the relative abundance of host and microbial community assembly in AMD of copper mines and polymetallic mines. Our results highlight the importance of viruses in shaping the microbial community from the individual host level to the community level.

Heavy metal pollution affected the stability and function of soil ecosystem. The impact of heavy metals on soil microbial community and the interaction of microbial community has been widely studied, but little was known about the response of community assembly to the heavy metal pollution. In this study, we collected 30 soil samples from non (CON), moderately (CL) and severely (CH) contaminated fields. The prokaryotic community was studied using high-throughput Illumina sequencing of 16s rRNA gene amplicons, and community assembly were quantified using phylogenetic-bin-based null approach (iCAMP). Results showed that diversity and composition of both bacterial and archaeal community changed significantly in response to heavy metal pollution. The microbial community assembly tended to be more deterministic with the increase of heavy metal concentration. Among the assembly processes, the relative importance of homogeneous selection (deterministic process) increased significantly (increased by 16.2%), and the relative importance of drift and dispersal limitation (stochastic process) decreased significantly (decreased by 11.4% and 5.4%, respectively). The determinacy of bacterial and archaeal community assembly also increased with heavy metal stress, but the assembly models were different. The deterministic proportion of microorganisms tolerant to heavy metals, such as Thiobacillus, Euryarchaeota and Crenarchaeota (clustered in bin 32, bin59 and bin60, respectively) increased, while the stochastic proportion of microorganisms sensitive to heavy metals, such as Koribacteraceae (clustered in bin23) increased. Therefore, the heavy metal stress made the prokaryotic community be deterministic, however, the effects on the assembly process of different microbial groups differed obviously., (Copyright © 2022 Elsevier Inc. All rights reserved.)

The root phenotypic traits have been considered as important factors in shaping the rhizosphere microbiome and regulating plant growth. However, the relationships between root phenotypic traits and the rhizosphere bacterial community remain unclear. We investigated two fields with different developing tobacco roots by a long-term positioning test in Hengshi. The well-developed root system (WDR) showed much more superiority in root phenotypic traits, including total root length, total projection area, surface area, and root tip number, than the underdeveloped root system. The specific root traits in WDR provided more ecological niches for the rhizosphere microorganisms, contributing to a more diverse microbial community and a more complex microbial network. The total root length and root tip number were the key factors shaping bacterial communities in the rhizosphere. In turn, the phyla Acidobacteria and Bacteroidetes might play vital roles in modifying root development and promoting plant growth according to their positive correlation with root phenotypic traits. Linking root phenotypic traits to the microbiome may enhance our understanding of rhizospheric interactions and their roles in developing rhizosphere ecosystems., (© 2022. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Understanding interactions within the gut microbiome and its stability are of critical importance for deciphering ecological issues within the gut ecosystem. Recent studies indicate that long-term instability of gut microbiota is associated with human diseases, and recovery of stability is helpful in the return to health. However, much less is known about such topics in fish, which encompass nearly half of all vertebrate diversity. Here, we examined the assembly and succession of gut microbiota in more than 550 zebrafish, and evaluated the variations of microbial interactions and stability across fish development from larva to adult using molecular ecological network analysis. We found that microbial interactions and stability in the fish gut ecosystem generally increased with host development. This could be attributed to the development of the zebrafish immune system, the increasing amount of space available for microbial colonization within the gut, and the greater stability of nutrients available for the colonized microbiota in adult zebrafish. Moreover, the potential keystone taxa, even those with relatively low abundances, played important roles in affecting the microbial interactions and stability. These findings indicate that regulating rare keystone taxa in adult fish may have great potential in gut microbial management to maintain gut ecosystem stability, which could also provide references for managing gut microbiota in humans and other animals. IMPORTANCE Understanding gut microbial stability and the underlying mechanisms is an important but largely ignored ecological issue in vertebrate fish. Here, using a zebrafish model and network analysis of the gut microbiota we found that microbial interactions and stability in the gut ecosystem increase with fish development. This finding has important implications for microbial management to maintain gut homeostasis and provide better gut ecosystem services for the host. First, future studies should always consider using fish of different age groups to gain a full understanding of gut microbial networks. Second, management of the keystone taxa, even those that are only present at a low abundance, during the adult stage may be a viable pathway to maintain gut ecosystem stability. This study greatly expands our current knowledge regarding gut ecosystem stability in terms of ecological networks affected by fish development, and also highlights potential directions for gut microbial management in humans and other animals.

Sulfate-reducing bacteria (SRB) are key players in many passive and active systems dedicated to the treatment of hydrometallurgical leachates. One of the main factors reducing the efficiency and activity of SRB is the low pH and poor nutrients in leachates. We propose an innovative solution utilizing biogenic ammonia (B-NH 3 ), produced by urea degrading bacteria, as a pretreatment agent for increasing the pH of the leachate and spontaneously stimulating SRB activity via bacterial secondary metabolites. The selected strain, Ochrobactrum sp. POC9, generated 984.7 mg/L of ammonia in 24 h and promotes an effective neutralization of B-NH 3 . The inferred metabolic traits indicated that the Ochrobactrum sp. POC9 can synthesize a group of vitamins B, and the production of various organic metabolites was confirmed by GC-MS analysis. These metabolites comprise alcohols, organic acids, and unsaturated hydrocarbons that may stimulate biological sulfate reduction. With the pretreatment of B-NH 3 , sulfate removal efficiency reached ~92.3% after 14 days of incubation, whereas SRB cell count and abundance were boosted (~10 7  cell counts and 88 OTUs of SRB) compared to synthetic ammonia (S-NH 3 ) (~10 3  cell counts and 40 OTUs of SRB). The dominant SRB is Desulfovibrio in both S-NH 3 and B-NH 3 pretreated leachate, however, it belonged to two different clades. By reconstructing the ecological network, we found that B-NH 3 not only directly increases SRB performance but also promotes other strains with positive correlations with SRB., (Copyright © 2021 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

In this study soils at different depths were collected in a Zn smelting site located in Zhuzhou City, China, in order to understand toxic metal(loid)s distribution and microbial community in vertical soil profile at a smelting site. Except Soil properties and metal(loid)s content, the richness and diversity of microbial communities in soil samples were analyzed via high-throughput Illumina sequencing of 16s rRNA gene amplicons. The results showed that the content of As, Pb, Cu, Cd, Zn, and Mn was relatively high in top soil in comparison to subsoil, while the concentration of Cr in subsoil was comparable with that in top soil due to its relative high background value in this soil layer. The bioavailability of Cd, Mn, Zn, and Pb was relative higher than that of As, Cr, and Cu. The diversity of soil microbial communities decreased with increasing depth, which might be ascribed to the decrease in evenness with increase in depth duo to the influence by environmental conditions, such as pH, TK (total potassium), CEC (cation exchange capacity), ORP (oxidation reduction potential), and Bio-Cu (bioavailable copper). The results also found Acidobacteria , Proteobacteria , Firmicutes , and Chloroflexi were dominant phyla in soil samples. At the genus level, Acinetobacter , Pseudomonas , and Gp7 were dominant soil microorganism. Besides, Environmental factors, such as SOM (soil organic matter), pH, Bio-Cu, Bio-Cd (bioavailable cadmium), and Bio-Pb (bioavailable lead), greatly impacted microbial community in surface soil (1-3 m), while ORP, TK, and AN concentration influenced microbial community in the subsoil (4-10 m).

Background: Graphene oxide (GO) has been suggested as an efficient assistant additive to eliminate non-specific amplification of the polymerase chain reaction (PCR). Although many studies have focused on exploring its molecular mechanism, the practice of GO on the quantitation of microbial community has not been implemented yet. In this study, GO was added in PCR system to explore the changes on removing typical amplification errors, such as chimera and mismatches on two kinds of mock communities (an evenly mixed and a staggered mock communities) and environmental samples., Results: High-throughput sequencing of bacterial and fungal communities, based on 16S rRNA genes and internal transcribed spacers (ITS) respectively, showed that GO could significantly increase large segmental error (chimeric sequence) in PCR procedure while had no specific effect on point error (mismatched sequence). Besides, GO reduced the α-diversity of community, and changed the composition of fungal community more obviously than bacterial community., Conclusions: Our study provides the first quantitative data on microbial community level to prove the negative effect of GO, and also indicates that there may be a more complex interaction between GO and comprehensive DNA fragments in PCR process.

The susceptibility of soil organic carbon (SOC) in tundra to microbial decomposition under warmer climate scenarios potentially threatens a massive positive feedback to climate change, but the underlying mechanisms of stable SOC decomposition remain elusive. Herein, Alaskan tundra soils from three depths (a fibric O horizon with litter and course roots, an O horizon with decomposing litter and roots, and a mineral-organic mix, laying just above the permafrost) were incubated. Resulting respiration data were assimilated into a 3-pool model to derive decomposition kinetic parameters for fast, slow, and passive SOC pools. Bacterial, archaeal, and fungal taxa and microbial functional genes were profiled throughout the 3-year incubation. Correlation analyses and a Random Forest approach revealed associations between model parameters and microbial community profiles, taxa, and traits. There were more associations between the microbial community data and the SOC decomposition parameters of slow and passive SOC pools than those of the fast SOC pool. Also, microbial community profiles were better predictors of model parameters in deeper soils, which had higher mineral contents and relatively greater quantities of old SOC than in surface soils. Overall, our analyses revealed the functional potential of microbial communities to decompose tundra SOC through a suite of specialized genes and taxa. These results portray divergent strategies by which microbial communities access SOC pools across varying depths, lending mechanistic insights into the vulnerability of what is considered stable SOC in tundra regions.

In order to explore the microbial communities and functions in distinct environments of acid mine drainage (AMD) ecosystem and fully comprehend the patterns of AMD formation and development, high-throughput sequencing technology was used to study the prokaryotic community composition in AMD puddles and surrounding rills in a mining area in Mengzi, Yunnan Province, China. By combining with physicochemical properties of the samples, we distinguished the key factors affecting the community structure and analyzed the environmental functions of the microflora. We discovered that the main phyla in AMD puddles were Euryarchaeota, Proteobacteria (including the class α-, γ- and δ-Proteobacteria), Nitrospirae, Firmicutes, Actinobacteria, and Acidobacteria. Community structure of the AMD puddles apparently differed from that of the surrounding rills. Microbial diversity was significantly positively correlated with pH, whereas the relative abundance of Thermoplasmata was negatively correlated with pH and this class might play a predominant role in community structure. There was high relative abundance of the genus Ferroplasma (6.60%-86.34%) in different samples of AMD puddles. Acidithiobacillus spp. were the major iron- and/or sulfur-oxidizing bacteria in AMD solutions and sediments, whereas relative abundance of the obligate iron-oxidizer Leptospirillum spp. was lower, and Ferrovum spp. were almost only present in the AMD solutions. In addition, acidophilic or acid-tolerant heterotrophic bacteria were widely distributed in the AMD solutions and sediments, which might promote the growth of iron- and/or sulfur-oxidizers and catalyze the oxidative/reductive dissolution of metal ores. Our results suggested that pH significantly impacted the microbial community structure of AMD environment by affecting the microbial diversity and microflora distribution.

A profound concern in developing microbially-assisted phytoextraction is that introduced microbes not only remove heavy metals from contaminated soils but also enhance metal uptake into plant tissues from the treated soils. Cadmium (Cd) removal efficiencies were compared after leaching with deionized water (CK), acidified basal salts medium (acid control), cell-free spent medium (spent bioleaching) and mixotrophic acidophiles (two-step bioleaching). Two-step bioleaching using the mixotrophic acidophiles removed 34% of total Cd and 87% of available Cd, significantly more than CK (3% and 4%), acid control (12% and 51%) and spent bioleaching (26% and 75%). Pot experiments of water spinach growing in four treated soils were conducted to evaluate the Cd uptake performance in plants. Notably, the mixotrophic acidophiles increased Cd concentration in plant tissues by 78% compared to the CK group. More interestingly, the mixotrophic acidophiles were not colonized in soils but caused the compositional increase of indigenous microbes such as the genera of Alicyclobacillus, Clostridium sensu strict and Streptacidiphilus. Meanwhile, two-step bioleaching had little effects on soil structure and physicochemical properties determined by the spectroscopy characteristics analysis. These results implied that the mixotrophic acidophiles facilitated the development of microbially-assisted phytoextraction technology., (Copyright © 2018. Published by Elsevier B.V.)

Background: The interaction mechanism between microbial communities and environment is a key issue in microbial ecology. Microbial communities usually change significantly under environmental stress, which has been studied both phylogenetically and functionally, however which method is more effective in assessing the relationship between microbial communities shift and environmental changes still remains controversial., Results: By comparing the microbial taxonomic and functional shift pattern along heavy metal contamination gradient, we found that both sedimentary composition and function shifted significantly along contamination gradient. For example, the relative abundance of Geobacter and Fusibacter decreased along contamination gradient (from high to low), while Janthinobacterium and Arthrobacter increased their abundances. Most genes involved in heavy metal resistance (e.g., metc, aoxb and mer) showed higher intensity in sites with higher concentration of heavy metals. Comparing the two shift patterns, there were correlations between them, because functional and phylogenetic β-diversities were significantly correlated, and many heavy metal resistance genes were derived from Geobacter, explaining their high abundance in heavily contaminated sites. However, there was a stronger link between functional composition and environmental drivers, while stochasticity played an important role in formation and succession of phylogenetic composition demonstrated by null model test., Conclusions: Overall our research suggested that the responses of functional traits depended more on environmental changes, while stochasticity played an important role in formation and succession of phylogenetic composition for microbial communities. So profiling microbial functional composition seems more appropriate to study the relationship between microbial communities and environment, as well as explore the adaptation and remediation mechanism of microbial communities to heavy metal contamination.

Background: Metagenomics allows us to acquire the potential resources from both cultivatable and uncultivable microorganisms in the environment. Here, shotgun metagenome sequencing was used to investigate microbial communities from the surface layer of low grade copper tailings that were industrially bioleached at the Dexing Copper Mine, China. A bioinformatics analysis was further performed to elucidate structural and functional properties of the microbial communities in a copper bioleaching heap., Results: Taxonomic analysis revealed unexpectedly high microbial biodiversity of this extremely acidic environment, as most sequences were phylogenetically assigned to Proteobacteria, while Euryarchaeota-related sequences occupied little proportion in this system, assuming that Archaea probably played little role in the bioleaching systems. At the genus level, the microbial community in mineral surface-layer was dominated by the sulfur- and iron-oxidizing acidophiles such as Acidithiobacillus-like populations, most of which were A. ferrivorans-like and A. ferrooxidans-like groups. In addition, Caudovirales were the dominant viral type observed in this extremely environment. Functional analysis illustrated that the principal participants related to the key metabolic pathways (carbon fixation, nitrogen metabolism, Fe(II) oxidation and sulfur metabolism) were mainly identified to be Acidithiobacillus-like, Thiobacillus-like and Leptospirillum-like microorganisms, indicating their vital roles. Also, microbial community harbored certain adaptive mechanisms (heavy metal resistance, low pH adaption, organic solvents tolerance and detoxification of hydroxyl radicals) as they performed their functions in the bioleaching system., Conclusion: Our study provides several valuable datasets for understanding the microbial community composition and function in the surface-layer of copper bioleaching heap.

Response of biological communities to environmental stresses is a critical issue in ecology, but how microbial communities shift across heavy metal gradients remain unclear. To explore the microbial response to heavy metal contamination (e.g., Cr, Mn, Zn), the composition, structure and functional potential of sedimentary microbial community were investigated by sequencing of 16S rRNA gene amplicons and a functional gene microarray. Analysis of 16S rRNA sequences revealed that the composition and structure of sedimentary microbial communities changed significantly across a gradient of heavy metal contamination, and the relative abundances were higher for Firmicutes, Chloroflexi and Crenarchaeota, but lower for Proteobacteria and Actinobacteria in highly contaminated samples. Also, molecular ecological network analysis of sequencing data indicated that their possible interactions might be enhanced in highly contaminated communities. Correspondently, key functional genes involved in metal homeostasis (e.g., chrR, metC, merB), carbon metabolism, and organic remediation showed a higher abundance in highly contaminated samples, indicating that bacterial communities in contaminated areas may modulate their energy consumption and organic remediation ability. This study indicated that the sedimentary indigenous microbial community may shift the composition and structure as well as function priority and interaction network to increase their adaptability and/or resistance to environmental contamination.

Temperature is an important correlate of global patterns of biodiversity, yet the mechanisms driving these relationships are not well understood. Taxa-area relationships (TARs) have been intensively examined, but the effects of temperature on TARs, particularly for microbial communities, are largely undocumented. Here we present a continental-scale description of temperature-dependent nested TARs of microbial communities (bacteria and archaea) from soils of six forest sites spanning a temperature gradient from subalpine Colorado to tropical Panama. Our results revealed that spatial scaling rates (z-values) of microbial communities varied with both taxonomic resolutions and phylogenetic groups. Additionally, microbial TAR z-values increased with temperature (r = 0.739, P < 0.05), but were not correlated with other environmental variables tested (P > 0.05), indicating that microbial spatial scaling rate is temperature-dependent. Understanding how temperature affects the spatial scaling of microbial biodiversity is of fundamental importance for preservation of soil biodiversity and management of ecosystems.