Rare prokaryotic sub-communities dominate the complexity of ecological networks and soil multinutrient cycling during long-term secondary succession in China's Loess Plateau

Rare biosphere drives deterministic community assembly, co-occurrence network stability, and system performance in industrial wastewater treatment system

Bacterial community is strongly associated with activated sludge performance, but there still remains a knowledge gap regarding the rare bacterial community assembly and their influence on the system performance in industrial wastewater treatment plants (IWWTPs). Here, we investigated bacterial communities in 11 full-scale IWWTPs with similar process designs, aiming to uncover ecological processes and functional traits regulating abundant and rare communities. Our findings indicated that abundant bacterial community assembly was governed by stochastic processes; thereby, abundant taxa are generally present in wastewater treatment compartments across different industrial types. On the contrary, rare bacterial taxa were primarily driven by deterministic processes (homogeneous selection 61.9%-79.7%), thus they only exited in specific IWWTPs compartments and wastewater types. The co-occurrence networks analysis showed that the majority of keystone taxa were rare bacterial taxa, with rare taxa contributing more to network stability. Furthermore, rare bacteria rather than abundant bacteria in the oxic compartment contributed more to the degradation of xenobiotics compounds, and they were main potential drivers of pollutant removal. This study demonstrated the irreplaceable roles of rare bacterial taxa in maintaining system performance of IWWTPs, and called for environmental engineers and microbial ecologists to increase their attention on rare biosphere.

Deciphering the environmental adaptation and functional trait of core and noncore bacterial communities in impacted coral reef seawater

Microorganisms play pivotal roles in different biogeochemical cycles within coral reef waters. Nevertheless, our comprehension of the microbially mediated processes following environmental perturbation is still limited. To gain a deeper insight into the environmental adaptation and nutrient cycling, particularly within core and noncore bacterial communities, it is crucial to understand reef ecosystem functioning. In this study, we delved into the microbial community structure and function of seawater in a coral reef under different degrees of anthropogenic disturbance. To achieve this, we harnessed the power of 16S rRNA gene high-throughput sequencing and metagenomics techniques. The results showed that a continuous temporal succession but little spatial heterogeneity in the bacterial communities of core and noncore taxa and functional profiles involved in nitrogen (N) and phosphorus (P) cycling. Eutrophication state (i.e., nutrient concentration and turbidity) and temperature played pivotal roles in shaping both the microbial community composition and functional traits of coral reef seawater. Within this context, the core subcommunity exhibited a remarkably broader habitat niche breadth, stronger phylogenetic signal and lower environmental sensitivity when compared to the noncore taxa. Null model analysis further revealed that the core subcommunity was governed primarily by stochastic processes, while deterministic processes played a more significant role in shaping the noncore subcommunity. Furthermore, our observations indicated that changes in function related to N cycling were correlated to the variations in noncore taxa, while core taxa played a more substantial role in critical processes such as P cycling. Collectively, these findings facilitated our knowledge about environmental adaptability of core and noncore bacterial taxa and shed light on their respective roles in maintaining diverse nutrient cycling within coral reef ecosystems.

Strategies for regulating the intensity of different cyanobacterial blooms: Insights from the dynamics and stability of bacterioplankton communities

The occurrence of cyanobacterial blooms is increasing in frequency and magnitude due to climate change and human activities, which poses a direct threat to drinking water security. The impacts of abiotic and biotic factors on the development of blooms have been well studied; however, control strategies for different bloom intensities have rarely been explored from the perspective of the dynamics and stability of bacterioplankton communities. Here, a network analysis was used to investigate the interactions and stability of microbial communities during different periods of R. raciborskii bloom in an inland freshwater lake. The abundance and diversity of rare taxa were significantly higher than that of abundant taxa throughout the bloom cycle. At the pre-bloom (PB) stage, microbial interactions among the different bacterial groups were weak but strongly negatively correlated, indicating low robustness and weak disturbance resistance within the community. However, community stability was better, and microbial interactions became more complicated at the high-bloom (HB) and low-bloom (LB) stages. Interestingly, rare taxa were significantly responsible for community stability and connectivity despite their low relative abundance. The Mantel test revealed that Secchi depth (SD), orthophosphate (PO43--P), and dissolved oxygen (DO) were significantly positively correlated with abundant taxa, rare taxa and PB. DO was significantly positively correlated with HB, intermediate taxa, and rare taxa, while water temperature (WT), N/P and total nitrogen (TN) were significantly positively correlated with LB, abundant taxa, intermediate taxa, and rare taxa. These findings suggest that reducing the PO43--P concentration at the PB stage may be an effective approach to preventing the development of R. raciborskii blooms, while regulating rare taxa at the HB and LB stages may be a key factor in controlling R. raciborskii blooms.

Progress on network modeling and analysis of gut microecology: a review

The gut microecological network is a complex microbial community within the human body that plays a key role in linking dietary nutrition and host physiology. To understand the complex relationships among microbes and their functions within this community, network analysis has emerged as a powerful tool. By representing the interactions between microbes and their associated omics data as a network, we can gain a comprehensive understanding of the ecological mechanisms that drive the human gut microbiota. In addition, the network-based approach provides a more intuitive analysis of the gut microbiota, simplifying the study of its complex dynamics and interdependencies. This review provides a comprehensive overview of the methods used to construct and analyze networks in the context of gut microecological background. We discuss various types of network modeling approaches, including co-occurrence networks, causal networks, dynamic networks, and multi-omics networks, and describe the analytical techniques used to identify important network properties. We also highlight the challenges and limitations of network modeling in this area, such as data scarcity and heterogeneity, and provide future research directions to overcome these limitations. By exploring these network-based methods, researchers can gain valuable insights into the intricate relationships and functional roles of microbial communities within the gut, ultimately advancing our understanding of the gut microbiota's impact on human health.

Niche differentiation and biogeography of Bathyarchaeia in paddy soil ecosystems: a case study in eastern China

Bathyarchaeia (formerly Bathyarchaeota) is a group of highly abundant archaeal communities that play important roles in global biogeochemical cycling. Bathyarchaeia is predominantly found in sediments and hot springs. However, their presence in arable soils is relatively limited. In this study, we aimed to investigate the spatial distributions and diversity of Bathyarchaeia in paddy soils across eastern China, which is a major rice production region. The relative abundance of Bathyarchaeia among total archaea ranged from 3 to 68% in paddy soils, and Bathy-6 was the dominant subgroup among the Bathyarchaeia (70-80% of all sequences). Bathyarchaeia showed higher migration ability and wider niche width based on the neutral and null model simulations. Bathy-6 was primarily assembled by deterministic processes. Soil pH and C/N ratio were identified as key factors influencing the Bathyarchaeia composition, whereas C/N ratio and mean annual temperature influenced the relative abundance of Bathyarchaeia. Network analysis showed that specific Bathyarchaeia taxa occupied keystone positions in the archaeal community and co-occurred with some methanogenic archaea, including Methanosarcina and Methanobacteria, and ammonia-oxidizing archaea belonging to Nitrososphaeria. This study provides important insights into the biogeography and niche differentiation of Bathyarchaeia particularly in paddy soil ecosystems.

Responses of microbial communities subjected to hydrodynamically induced disturbances in an organic contaminated site

Organic contaminated sites have gained significant attention as a prominent contributor to shallow groundwater contamination. However, limited knowledge exists regarding the impact of hydrodynamic effects on microbially mediated contaminant degradation at such sites. In this study, we investigated the distribution characteristics and community structure of prokaryotic microorganisms at the selected site during both wet and dry seasons, with a particular focus on their environmental adaptations. The results revealed significant seasonal variations (P < 0.05) in the α-diversity of prokaryotes within groundwater. The dry season showed more exclusive OTUs than the wet season. The response of prokaryotic metabolism to organic pollution pressure in different seasons was explored by PICRUSt2, and enzymes associated with the degradation of organic pollutants were identified based on the predicted functions. The results showed that hormesis was considered as an adaptive response of microbial communities under pollution stress. In addition, structural equation models demonstrated that groundwater level fluctuations can, directly and indirectly, affect the abundance and diversity of prokaryotes through other factors such as oxidation reduction potential (ORP), dissolved oxygen (DO), and naphthalene (Nap). Overall, our findings imply that the taxonomic composition and functional properties of prokaryotes in groundwater in organic contaminated sites is influenced by the interaction between seasonal variations and characteristics of organic pollution. The results provide new insights into microbiological processes in groundwater systems in organic contaminated sites.

Intermediate irrigation with low fertilization promotes soil nutrient cycling and reduces CO2 and CH4 emissions via regulating fungal communities in arid agroecosystems

The field practices, including irrigation and fertilization, strongly affect greenhouse gas emissions and soil nutrient cycling from agriculture. Understanding the underlying mechanism of greenhouse gas emissions, soil nutrient cycling, and their impact factors (fungal diversity, network characteristics, soil pH, salt, and moisture) is essential for efficiently managing global greenhouse gas mitigation and agricultural production. By considering abundant and rare taxa, we determine the identities and relative importance of ecological processes that modulate the fungal communities and identify whether they are crucial contributors to soil nutrient cycling and greenhouse gas emissions. The research is based on a 4-year field fertigation experiment with low (300 kg/ha P2O5 with 150 kg/ha urea) and high (600 kg/ha P2O5 with 300 kg/ha urea) fertilization level and three irrigation levels, that is, low (200 mm), medium (300 mm), and high (400 mm). The α-diversity (richness and Shannon index) of fungal subcommunities was significantly higher under medium irrigation (300 mm) and low fertilization (300 kg/ha P2O5 with 150 kg/ha urea) than under other treatments. Intermediate irrigation with low fertilization treatment yielded the most significant higher multinutrient cycling index and the lowest CO2 and CH4 emissions. The null model indicated that abundant taxa are mainly regulated by stochastic processes (dispersal limitation), and rare taxa are mainly regulated by environmental selection, especially by soil salinity. The co-occurrence network of rare taxa explained the changes in the entire fungal network stability. The abundant taxa played vital roles in regulating soil nutrient status, owing to the stronger association between their network and multinutrient cycling index. Furthermore, we have confirmed that soil moisture and fungal network stability are crucial factors affecting greenhouse gas emissions. Together, these results provide a deep understanding of the mechanisms that reveal fungal community assembly and soil fungal-driven variations in nutrient status and network stability, link fungal network characteristics to ecosystem functions, and reveal the factors that influence greenhouse gas emissions.

Identification and relative contributions of environmental driving factors for abundant and rare bacterial taxa to thermal stratification evolution

The thermal stratification of reservoir affects water quality, and water quality evolution is largely driven by microorganisms. However, few studies have been conducted on the response of abundant taxa (AT) and rare taxa (RT) to thermal stratification evolution in reservoirs. Here, using high-throughput absolute quantitative techniques, we examined the classification, phylogenetic diversity patterns, and assembly mechanisms of different subcommunities during different periods and investigated the key environmental factors driving community construction and composition. The results showed that community and phylogenic distances of RT were higher than AT (P < 0.001), and community and phylogenic distances of the different subcommunities were significantly positively correlated with the dissimilarity of environmental factors (P < 0.001). Nitrate (NO₃^--N) was the main driving factor of AT and RT in the water stratification period, and Mn was the main driving factor in the water mixing period (MP) based on redundancy analysis (RDA) and random forest analysis (RF). The interpretation rate of key environmental factors based on the selected indicator species in RT by RF was higher than that of AT, and Xylophilus (10.5%) and Prosthecobacter (0.1%) had the highest average absolute abundance in AT and RT during the water stable stratification period (SSP), whereas Unassigned had the highest abundance during the MP and weak stratification period (WSP). The network of RT and environmental factors was more stable than that of AT, and stratification made the network more complex. NO₃^--N was the main node of the network during the SSP, and manganese (Mn) was the main node during the MP. Dispersal limitation dominated community aggregation, the proportion of AT was higher than that of RT. Structural Equation Model (SEM) showed that NO₃^--N and temperature (T) had the highest direct and total effects on β-diversity of AT and RT for the SP and MP, respectively.

Unexpected enrichment of antibiotic resistance genes and organic remediation genes in high-altitude lakes at Eastern Tibetan Plateau

Elevation has a strong effect on aquatic microbiome. However, we know little about the effects of elevation on functional genes, especially antibiotic resistance genes (ARGs) and organic remediation genes (ORGs) in freshwater ecosystems. In this study, we analyzed five classes of functional genes including ARGs, metal resistance genes (MRGs), ORGs, bacteriophages, and virulence genes between two high-altitude lakes (HALs) and two low-altitude lakes (LALs) in Mountain Siguniang at Eastern Tibetan Plateau by means of GeoChip 5.0. No differences (Student's t-test, p > 0.05) of gene richness including ARGs, MRGs, ORGs, bacteriophages, and virulence genes in HALs and LALs were found. The abundance of most ARGs and ORGs was higher in HALs than in LALs. For MRGs, the abundance of macro metal resistance genes of potassium, calcium, and aluminum was higher in HALs than in LALs (Student's t-test, p < 0.05; all Cohen's d > 0.8). The abundance of some heavy metal resistance genes of lead and mercury was lower in HALs than in LALs (Student's t-test, p < 0.05; all Cohen's d < -0.8). The composition of these functional genes in HALs differed significantly from in LALs. The functional gene network in HALs was also more complex than that in LALs. We speculate that enrichment of ARGs and ORGs in HALs is related to different microbial communities, exogenous ARGs, and enriched persistent organic pollutants through long-range atmospheric transport driven by the Indian monsoon. This study highlights the unexpected enrichment of ARGs, MRGs, and ORGs in remote lakes at high elevations.

Distinct distribution patterns and functional potentials of rare and abundant microorganisms between plastisphere and soils

The increasing application of plastic film has caused the "white pollution" of farmlands in greenhouses. To date, most studies on the ecology of the plastisphere have focused on the whole microbial community, with few on the rare and abundant taxa, especially in the terrestrial ecosystems. To understand the plastisphere rare and abundant taxa of bacterial and fungal communities, we collected residues of plastic film from plastic-covered soils in the greenhouse. The plastisphere was significantly different from surrounding soils in terms of alpha- and beta-diversities of abundant and rare taxa. Such discrepancies were greater in rare taxa than in abundant taxa. Besides, the enrichment of soil-borne plant pathogenic fungi in the plastisphere implied that plastic film residues can act as vectors for pathogen transmission. In the plastisphere, the stochastic process governed the assemblies of rare taxa, while deterministic assemblies dominated that of abundant taxa. However, in surrounding soils, the stochastic process played a larger role in abundant taxa as compared to rare taxa. The plastisphere showed a network of less complexity, more competitive connections, and more modules compared to surrounding soils, and rare taxa played greater roles than abundant taxa. There existed obvious discrepancies in the microbial functions between surrounding soils and plastisphere, including carbon, sulfur, nitrogen, and phosphorus cycling, and rare taxa contribute large proportions to the above cycling processes. Altogether, the findings advance our understanding of ecological mechanisms of abundant and rare taxa in the plastisphere in terrestrial ecosystems.

Deciphering the distinct successional patterns and potential roles of abundant and rare microbial taxa of urban riverine plastisphere

Microbial colonization on microplastics has provoked global concern; however, many studies have not considered the successional patterns and potential roles of abundant and rare taxa of the plastisphere during colonization. Hence, we investigate the taxonomic composition, assembly, interaction and function of abundant and rare taxa in the riverine plastisphere by conducting microcosm experiments. Results showed that rare taxa occupied significantly high community diversity and niche breadth than the abundant taxa, which implies that rare taxa are essential components in maintaining the community stability of the plastisphere. However, the abundant taxa played a major role in driving the succession of plastisphere communities during colonization. Both stochastic and deterministic processes signally affected the plastisphere community assemblies; while, the deterministic patterns (heterogeneous selection) were especially pronounced for rare biospheres. Plastisphere microbial networks were shaped by the enhancement of network modularity and reinforcement of positive interactions. Rare taxa played critical roles in shaping stable plastisphere by occupying the key status in microbial networks. The strong interaction of rare and non-rare taxa suggested that multi-species collaboration might be conducive to the formation and stability of the plastisphere. Both abundant and rare taxa were enriched with plentiful functional genes related to carbon, nitrogen, phosphorus and sulfur cycling; however, their potential metabolic functions were significantly discrepant, implying that the abundant and rare microbes may play different roles in ecosystems. Overall, this study strengthens our comprehending of the mechanisms regarding the formation and maintenance of the plastisphere.

The contrasting responses of abundant and rare microbial community structures and co-occurrence networks to secondary forest succession in the subalpine region

Knowledge of variations in abundant and rare soil microbial communities and interactions during secondary forest succession is lacking. Soil samples were gathered from different secondary successional stages (grassland, shrubland, and secondary forest) to study the responses of abundant and rare bacterial and fungal communities, interactions and driving factors to secondary forest succession by Illumina sequencing of the 16S and ITS rRNA genes. The results showed that the α-diversities (Shannon index) of abundant bacteria and fungi revealed no significant changes during secondary forest succession, but increased significantly for rare bacteria. The abundant and rare bacterial and fungal β-diversities changed significantly during secondary forest succession. Network analysis showed no obvious changes in the topological properties (nodes, links, and average degree) of abundant microbial networks during secondary forest succession. In contrast, these properties of the rare microbial networks in the secondary forest were higher than those in the grassland and shrubland, indicating that rare microbial networks are more responsive to secondary forest succession than abundant microorganisms. Additionally, rare microbial networks revealed more microbial interactions and greater network complexity than abundant microbial networks due to their higher numbers of nodes and links. The keystone species differed between the abundant and rare microbial networks and consisted of 1 and 48 keystone taxa in the abundant and rare microbial networks, respectively. Soil TP was the most important influencing factor of abundant and rare bacterial communities. Successional stages and plant richness had the most important influences on abundant and rare fungal communities, respectively. C:P, SM and N:P were mainly related to abundant and rare microbial network topological properties. Our study indicates that abundant and rare microbial communities, interactions and driving factors respond differently to secondary forest succession.

Weak environmental adaptation of rare phylotypes sustaining soil multi-element cycles in response to decades-long fertilization

Deciphering the ecological role of soil communities in the maintenance of multiple ecosystem functions is pivotal for the conservation and sustainability of soil biodiversity. However, few studies have investigated niche differentiation of abundant and rare microbiota, as well as their contributions to multiple soil elemental cycles, particularly in agroecosystems that have received decades of intense fertilization. Here, we characterized the environmental thresholds and phylogenetic signals for the environmental adaptation of both abundant and rare microbial subcommunities via amplicon sequencing and metagenomic sequencing and explored their importance in sustaining soil multiple nutrient cycling in agricultural fields that were fertilized for two decades. The results showed that rare taxa exhibited narrower niche breadths and weaker phylogenetic signals than abundant species. The assembly of abundant subcommunity was shaped predominantly by dispersal limitation (explained 71.1 % of the variation in bacteria) and undominated processes (explained 75 % of the variation in fungi), whereas the assembly of rare subcommunity was dominated by homogeneous selection process (explained 100 % of the variation in bacteria and 60 % of the variation in fungi). Soil ammonia nitrogen was the leading factor mediating the balance between stochastic and deterministic processes in both abundant (R² = 0.15, P < 0.001) and rare (R² = 0.08, P < 0.001) bacterial communities. Notably, the rare biosphere largely contributed to key soil processes such as carbon (R²_bacteria = 0.03, P < 0.05; R²_fungi = 0.05, P < 0.05) and nitrogen (R²_bacteria = 0.03, P < 0.05; R²_fungi = 0.17, P < 0.001) cycling. Collectively, these findings facilitate our understanding of the maintenance of rhizosphere bacterial and fungal diversity in response to agricultural fertilization and highlight the key role of rare taxa in sustaining agricultural ecosystem functions.

Kelp Culture Enhances Coastal Biogeochemical Cycles by Maintaining Bacterioplankton Richness and Regulating Its Interactions

As an important carbon sink, seaweed cultivation plays a vital role in controlling global climate change. However, most studies have been focused on the seaweed itself, and knowledge of bacterioplankton dynamics in seaweed cultivation activities is still limited. Here, a total of 80 water samples were obtained from a coastal kelp cultivation area and adjacent non-culture area in the seedling and mature stages. The bacterioplankton communities were analyzed using high-throughput sequencing of bacterial 16S rRNA genes, and the microbial genes involving biogeochemical cycles were measured by a high-throughput quantitative PCR (qPCR) chip. Seasonal variations in alpha diversity indices of bacterioplankton were found, and kelp cultivation mitigated this decline in biodiversity from the seedling to the mature stage. Further beta diversity and core taxa analyses revealed that the maintenance of biodiversity was due to kelp cultivation favoring the survival of rare bacteria. Comparisons of gene abundances between coastal water with and without kelp cultivation showed a more powerful capacity of biogeochemical cycles induced by kelp cultivation. More importantly, a positive relationship between bacterial richness and biogeochemical cycling functions was observed in samples with kelp cultivation. Finally, a co-occurrence network and pathway model indicated that the higher bacterioplankton biodiversity in kelp culture areas compared to non-mariculture regions could balance the microbial interactions to regulate biogeochemical cycles and thus enhance the ecosystem functions of kelp cultivation coasts. The findings of this study allow us to better understand the effects of kelp cultivation on coastal ecosystems and provide novel insights into the relationship between biodiversity and ecosystem functions. IMPORTANCE In this study, we tried to address the effects of seaweed cultivation on the microbial biogeochemical cycles and the underlying relationships between biodiversity and ecosystem functions. We revealed clear enhancement of biogeochemical cycles in the seaweed cultivation areas compared to the non-mariculture coasts at both the beginning and ending of the culture cycle. Moreover, the enhanced biogeochemical cycling functions in the culture areas were found to contribute to the richness and interspecies interactions of bacterioplankton communities. The findings of this study allow us to better understand the effects of seaweed cultivation on coastal ecosystems and provide novel insights into the relationship between biodiversity and ecosystem functions.

Consistent responses of coral microbiome to acute and chronic heat stress exposures

Frequent and intense heat waves lead to bleaching and even death of reef-building corals, and the thermal tolerance ultimately depends on the genetic composition of the holobiont. Here, we compared the effects of acute and chronic heat stress exposures on coral Porites cylindrica holobiont. Regardless of the temperature treatment, corals at 33 °C showed signs of bleaching and a significant decrease in photochemical efficiency (Fv/Fm). However, Symbiodiniaceae communities were relatively stable and all dominated by the same genus Cladocopium (C15). The relative abundanbce of core microbiome varied significantly, and they may provide several functions important to holobiont fitness. Both heat stress exposures induced the significant structural reorganization of coral-associated bacteria, with bacterial diversity and community heterogeneity significantly increasing with the temperature treatment. The modified stochasticity ratio (MST) revealed that stochastic processes dominated bacterial community assembly in thermally stressed corals. Certain core bacterial members that were hypothesized to fulfil functional niche decreased significantly, with the enrichment of potentially pathogenic and opportunistic bacteria in heat stress exposures. Thermally stressed corals had more positive correlation, higher network complexity and tighter associations among microbial taxa, relative to healthy corals. Overall, the coral microbiome exhibits similar responses to acute and chronic heat stress, and our study provides new insights about the deleterious impacts of complex warming oceans on coral holobiont.

Distinct Responses of Abundant and Rare Soil Bacteria to Nitrogen Addition in Tropical Forest Soils

Soil microbial responses to anthropogenic nitrogen (N) enrichment at the overall community level has been extensively studied. However, the responses of community dynamics and assembly processes of the abundant versus rare bacterial taxa to N enrichment have rarely been assessed. Here, we present a study in which the effects of short- (2 years) and long-term (13 years) N additions to two nearby tropical forest sites on abundant and rare soil bacterial community composition and assembly were documented. The N addition, particularly in the long-term experiment, significantly decreased the bacterial α-diversity and shifted the community composition toward copiotrophic and N-sensitive species. The α-diversity and community composition of the rare taxa were more affected, and they were more closely clustered phylogenetically under N addition compared to the abundant taxa, suggesting the community assembly of the rare taxa was more governed by deterministic processes (e.g., environmental filtering). In contrast, the abundant taxa exhibited higher community abundance, broader environmental thresholds, and stronger phylogenetic signals under environmental changes than the rare taxa. Overall, these findings illustrate that the abundant and rare bacterial taxa respond distinctly to N addition in tropical forests, with higher sensitivity of the rare taxa, but potentially broader environmental acclimation of the abundant taxa. IMPORTANCE Atmospheric nitrogen (N) deposition is a worldwide environmental problem and threatens biodiversity and ecosystem functioning. Understanding the responses of community dynamics and assembly processes of abundant and rare soil bacterial taxa to anthropogenic N enrichment is vital for the management of N-polluted forest soils. Our sequence-based data revealed distinct responses in bacterial diversity, community composition, environmental acclimation, and assembly processes between abundant and rare taxa under N-addition soils in tropical forests. These findings provide new insight into the formation and maintenance of bacterial diversity and offer a way to better predict bacterial responses to the ongoing atmospheric N deposition in tropical forests.

Urbanization increases stochasticity and reduces the ecological stability of microbial communities in amphibian hosts

Urbanization not only profoundly alters landscape profiles, ecosystems and vertebrate faunal diversity but also disturbs microbial communities by increasing stochasticity, vulnerability, biotic homogenization, etc. However, because of the buffering effect of host species, microbial communities are expected to be influenced by both host species and urbanization stresses. Therefore, the impacts of urbanization on animals' microbial symbionts could be more complex and uncertain. In this study, we quantified the urbanization degree of sampling sites and surveyed the gut and skin microbes of three amphibian host species in different sites in urban parks and nearby villages of Chengdu, Southwest China. Furthermore, a co-occurrence network analysis, the phylogenetic normalized stochasticity ratio and Sloan neutral community models were applied to infer the impact of urbanization on symbiotic microbial communities. For the three host species, urbanization increased the diversity of symbiotic microbes and the number of keystone microbial taxa. However, the negative effects of such increased diversification were evident, as the community stochasticity and co-occurrence network structure vulnerability also increased, while the network structure complexity and stability were reduced. Finally, the community stochasticity had positive associations with the network vulnerability, implying that the existence of many transient symbiotic rare microbial taxa in urban parks makes the symbiotic microbial community structure more fragile. Conclusively, urbanization increased the symbiotic microbial diversity at the cost of community stability; the results provide a new perspective for better understanding the complex triangulated environment-host-microbe relationship.

Changes in the bacterial communities in chromium-contaminated soils

Introduction

Hexavalent chromium or Cr(VI) is essential to various industries, such as leather manufacturing and stainless steel production. Given that inevitable leakage from industries pollutes the soil and thereby affects the soil environment. Microbial communities could improve the quality of the soil. Abundant bacterial communities would significantly enhance the soil richness and resist external pressure, benefiting agriculture. But the pollution of heavy metal broke the balance and decrease the abundance of bacterial communities, which weak the self-adjust ability of soil. This study aimed to explore changes in the diversity of soil bacterial communities and to identify the influences of soil bacterial communities on enzymes in soil polluted by Cr(VI).

Methods

The target soils were sampled quickly and aseptically. Their chromium content was detected through inductively coupled plasma-mass spectrometry, and bacterial microbiome communities were explored through MiSeq high-throughput sequencing. Then, the content of nitrite reductase and catalases were investigated through enzyme-linked immunosorbent assay (ELISA).

Results

Chromium content in polluted soils was higher than that in the control soils at all depths. Sobs, Chao1, Ace, and Shannon diversity estimators in the control were higher, whereas Simpson's diversity estimators in the control soils were lower than those of contaminated samples at all depths. Contaminants affected the composition of the bacterial community. The soil microbial species were relatively single and inhomogeneous in the polluted soils. The bacterial phyla in polluted and controlled soils include Proteobacteria, Actinobacteria, Chloroflexi, and Acidobacteria, which differ markedly in abundance.

Discussion

The results of these observations provide insights into the ecotoxicological effects of Cr(VI) exposure to soil microorganisms. To sum up these results are critical for evaluating the stabilized state of microbial community structures, contributing to the assessment of the potential risk of metal accumulation in soils.

The identification of the new species Nitratireductor thuwali sp. nov. reveals the untapped diversity of hydrocarbon-degrading culturable bacteria from the arid mangrove sediments of the Red Sea

Introduction

The geological isolation, lack of freshwater inputs and specific internal water circulations make the Red Sea one of the most extreme-and unique-oceans on the planet. Its high temperature, salinity and oligotrophy, along with the consistent input of hydrocarbons due to its geology (e.g., deep-sea vents) and high oil tankers traffic, create the conditions that can drive and influence the assembly of unique marine (micro)biomes that evolved to cope with these multiple stressors. We hypothesize that mangrove sediments, as a model-specific marine environment of the Red Sea, act as microbial hotspots/reservoirs of such diversity not yet explored and described.

Methods

To test our hypothesis, we combined oligotrophic media to mimic the Red Sea conditions and hydrocarbons as C-source (i.e., crude oil) with long incubation time to allow the cultivation of slow-growing environmentally (rare or uncommon) relevant bacteria.

Results and discussion

This approach reveals the vast diversity of taxonomically novel microbial hydrocarbon degraders within a collection of a few hundred isolates. Among these isolates, we characterized a novel species, Nitratireductor thuwali sp. nov., namely, Nit1536^T. It is an aerobic, heterotrophic, Gram-stain-negative bacterium with optimum growth at 37°C, 8 pH and 4% NaCl, whose genome and physiological analysis confirmed the adaptation to extreme and oligotrophic conditions of the Red Sea mangrove sediments. For instance, Nit1536^T metabolizes different carbon substrates, including straight-chain alkanes and organic acids, and synthesizes compatible solutes to survive in salty mangrove sediments. Our results showed that the Red Sea represent a source of yet unknown novel hydrocarbon degraders adapted to extreme marine conditions, and their discovery and characterization deserve further effort to unlock their biotechnological potential.

Microbial community succession in soils under long-term heavy metal stress from community diversity-structure to KEGG function pathways

Currently, understanding the structure and function of the microbial community is the key step in artificially constructing microbial communities to control soil heavy metal pollution. Abundant/rare microbial communities play different roles in different levels of concentrations. However, the correlation between heavy metals and rare/abundant subgroups is poorly understood. In this study, we used a metagenomics approach to comprehensively investigate the evolutionary changes in microbial diversity, structure, and function under different heavy metal concentration stress in soils surrounding gold tailings. The results show that the main pollutants were Pb, As, and Zn. Indigenous microorganisms have different responses to heavy metal concentrations. Bacteria are the main components of indigenous microorganisms, mainly including Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria. With the increase of heavy metal pollution, the relative abundance of Proteobacteria increased, and that of Actinobacteria decreased. Archaea was significantly inhibited by heavy metal stress and was more sensitive to heavy metal concentration. The response of fungi to heavy metal concentration was not obvious. The results of KEGG pathways showed that carbon fixation was inhibited with increasing heavy metal concentrations, while nitrogen metabolism was in contrast. Abundant subcommunity had a greater correlation mainly with metal resistance mechanisms, and rare subcommunity plays a key role for soil nutrient cycling such as N, S cycling in soils contaminated. Overall, this study provides a comprehensive analysis of the effects of heavy metal stress at different concentrations on microorganisms in farmland around gold tailings and reveals the relationship between heavy metals on KEGG pathways.

Characteristics of soil carbon emissions and bacterial community composition in peatlands at different stages of vegetation succession

Microorganisms are important components of soil ecosystems and play an important role in material cycles. Northern peatlands are important ecosystems in middle-high latitude regions. In peatlands, different vegetation successions occur with changes in groundwater levels. The overall carbon emission of peat bogs is related to the carbon stability of the surrounding environment. Unraveling the assembly and distribution of bacterial communities at different succession stages in peatland is essential to understanding the soil nutrient cycle. In this study, we investigated the characteristics of soil carbon emissions and the composition of subsurface microorganisms under six different succession stages. The highest carbon emission was observed in mossy peatlands, and their soil enzyme activity was closely related to the aboveground vegetation cover type. The succession pattern of ground vegetation was the main driver of soil microorganisms. The abundance of the dominant Proteobacteria decreased with increasing soil depth, while the opposite trend was observed for Chloroflexi. Furthermore, the community structure of microorganisms became progressively simpler and looser as soil water content decreased. The bacterial alpha diversity was driven by soil dissolved organic carbon and Fe, and the beta diversity was driven mainly by soil water content. The bacteria presented a random distribution in a nutrient-rich soil environment and shifted to deterministic distribution with decreasing water and nutrient contents. The balance between taxonomic diversity and dispersal limitation mediates species coexistence in the soil microbiome. This study provides new insights into the soil environment at different stages of succession in peatlands.

Deciphering the diversity patterns and community assembly of rare and abundant bacterial communities in a wetland system

Water microorganisms that have distinct contributions to community dynamics, including many rare taxa and few abundant taxa, are crucial to the wetland ecosystem functions. In this study, we comprehensively investigated the diversity patterns and assembly processes of rare and abundant taxa to strengthen our understanding of ecosystem function and diversity in a wetland system. The results showed that TN and NH₃-N were the most significant factors affecting the community structure in this wetland. Functional Annotation of Prokaryotic Taxa (FAPROTAX) revealed that functions associated with nitrogen removal were the most prevalent metabolic pathways in samples of regenerated wetland (RW). Co-occurrence network analysis revealed that nonrare taxa exhibited more interactions with rare taxa than with conspecifics and some microbial hubs belonged to rare taxa, which might play an instrumental role in maintaining the stability of the community structure. We found that the assembly of rare taxa with a lower niche breadth was mainly governed by homogeneous selection, implying that their higher sensitivity of these to environmental disturbances and changes in TN played significant roles in community assembly of rare taxa. In contrast, the assembly of abundant taxa with higher niche breadth was dominated by stochastic processes (undominated process and dispersal limitation) indicating that abundant taxa had greater responsibility for maintaining community structure when exposed to environmental fluctuations. These results broaden our understanding of the microbial structure, interactions and ecological assembly mechanisms underlying microbial dynamics in aquatic ecosystems, which are crucial for the management of microorganisms in the wetlands.

Enhancing network complexity and function of soil bacteria by thiourea-modified biochar under cadmium stress in post-mining area

Cadmium (Cd) pollution cause severe stress to soil microorganisms and biochar utilized for its ability to immobilize Cd in the soil effectively. However, the influence of biochar on the structure and function of the bacterial network under Cd stress is unclear. This research reports a pot experiment conducted to investigate the impact of 2.0% Italian poplar bark biochar (PB), 2.0% thiourea-modified biochar (TP), and control treatment (CK) on the complexity, stability and functional properties of the bacterial community under Cd stress. The results showed that: (1) Biochar increased the diversity of soil bacterial consortia under Cd stress (p < 0.05), and the diversity index demonstrated as order of CK < PB < TP; (2) Compared with CK network, the nodes number of PB and TP treatments networks were much higher, while the modularity and transitivity increased by 0.04% and 37.6%, 2.45% and 1.12%, respectively. The biochar amendment increased the stability and complexity of the network; (3) PICRUSt2 prediction results show that Xenobiotics biodegradation and metabolism membrane transport of TP treatment increased 62.52% and 53.62% compared with CK, respectively, which could be related to the decrease in Cd content according to principal component analysis. (4) The reduction of leaching Cd content caused network complexity and bacterial function changes by biochar amendment. TP amendment enhanced the complexity and stability of soil bacterial community under Cd stress, which will provide a scientific basis for in situ remediations of Cd-contaminated soils.

Biochar rebuilds the network complexity of rare and abundant microbial taxa in reclaimed soil of mining areas to cooperatively avert cadmium stress

Understanding the interactions between the soil microbial communities and species is critical in the remediation of heavy metal-contaminated soil. Biochar has been widely applied as a stabilizer in the in situ remediation of cadmium (Cd)-contaminated soils in mining areas. However, the rebuilding of the microbial taxa of rare and abundant species by biochar and their cooperative resistance to Cd stress remains elusive. In this pursuit, the present study envisaged the effects of two types of biochars viz., poplar bark biochar (PB) and thiourea-modified poplar bark biochar (TP) on the rare and abundant bacterial and fungal taxa by using pot experiments. The results demonstrated that the PB and TP treatments significantly reduced the leached Cd content, by 35.13 and 68.05%, respectively, compared with the control group (CK), in the reclaimed soil of the mining area. The application of biochar significantly improved the physicochemical properties like pH and Soil Organic Matter (SOM) of the soil. It was observed that TP treatment was superior to the PB and CK groups in increasing the diversity of the soil abundant and rare species of microbial taxa. Compared with the CK group, the application of PB and TP enhanced and elevated the complexity of the microbial networks of rare and abundant taxa, increased the number and types of network core microorganisms, reshaped the network core microorganisms and hubs, and boosted the microbial resistance to Cd stress. Our results indicate the response of rare and abundant microbial taxa to biochar application and the mechanism of their synergistic remediation of Cd-contaminated soil, thereby providing technical feasibility for in situ remediation of Cd-contaminated soil in mining areas.

Land use alters diazotroph community structure by regulating bacterivores in Mollisols in Northeast China

Changes in land use can generate environmental pressures that influence soil biodiversity, and numerous studies have examined the influences of land use on the soil microbial communities. However, little is known about the effects of land use on ecological interactions of soil microbes and their predators. Diazotrophs are key soil microbes that play important functional roles in fixing atmospheric nitrogen. In this study, we investigated the co-association of diazotroph community members and patterns of diazotroph and bacterivore networks under different long-term land uses including cropland, grassland, and bare land. Diazotroph community was characterized by high-throughput sequencing. The results indicated that land use type influenced the dominant genera of diazotrophs and shaped the occurrence of specific indicator diazotroph taxa. Co-existing pattern analysis of diazotrophs and bacterivores indicated that grassland converted from cropland increased the complexity of diazotroph and bacterivore network structure. The number of nodes for diazotrophs and bacterivores was higher in grassland than in cropland and bare land. Random forest analysis revealed that six bacterivore genera Cephalobus, Protorhabditis, Acrobeloides, Mesorhabditis, Anaplectus, and Monhystera had significant effects on diazotrophs. Bacterivores were found to have predominantly negative effects in bare land. Different bacterivores had differing effects with respect to driving changes in diazotroph community structure. Structural equation model showed that land use could control diazotroph community composition by altering soil properties and regulating abundance of bacterivores. These findings accordingly enhance our current understanding of mechanisms underlying the influence of land use patterns on diazotrophs from the perspective of soil food webs.

Abundant and rare soil fungi exhibit distinct succession patterns in the forefield of Dongkemadi glacier on the central Qinghai-Tibet Plateau

Glaciers are retreating rapidly, exposing extensive new soil habitats in glacier forefields and providing unique areas for studying primary succession. However, understanding the variation patterns and assembly mechanisms of abundant and rare fungi subcommunities along the glacier-retreating chronosequence remains a knowledge gap, especially true for the vast Qinghai-Tibet Plateau (QTP). Here, we investigated fungal communities in the glacier forefield in Dongkemadi Glaicer on the central QTP. The results showed that fungal alpha diversity exhibited a clear increasing pattern in response to increasing of distance to glacier. The percentage of abundant OTUs decreased while the percentage of rare OTUs increased, suggesting that soil development is more beneficial to the rare taxa. The distributions of both abundant and rare subcommunities exhibited a clear spatial pattern along the distance to glacier, and might be strongly controlled by multiple environmental variables, including pH, soil moisture, vegetation status, soil organic carbon, total nitrogen, and soluble reactive phosphorus. Abundant and rare fungal subcommunities were structured in different assembly regimes. Dispersal limitation processes were dominant for both abundant and rare subcommunities but with a stronger contribution to abundant subcommunity assembly. Heterogeneous selection processes contributed higher and non-dominant processes contributed lower to abundant subcommunities than to rare subcommunities. The modular structure of the fungal co-occurrence network was highly localized along the soil chronosequence. By revealing distinct diversity patterns and community assembly mechanisms of abundant and rare fungal subcommunities, our study improved our understanding of ecological succession along the glacier-retreating chronosequence.

A Stronger Rhizosphere Impact on the Fungal Communities Compared to the Bacterial Communities in Pecan Plantations

Understanding microbial communities associated with bulk and rhizosphere soils will benefit the maintenance of forest health and productivity and the sustainable development of forest ecosystems. Based on MiSeq sequencing, we explored the differences between the bulk soil and the rhizosphere soil on bacterial and fungal communities of pecan plantation. Results suggested that rhizosphere-associated fungal rather than bacterial community structures differed from bulk soil, and rhizosphere soil had lower fungal diversity than bulk soil. Actinobacteria and Cantharellales were the bacterial and fungal biomarkers of the rhizosphere soil of pecan plantation, respectively. In addition, Pleosporales, which are mainly involved in saprophylaxis and plant pathogenic processes, was identified as one of the most important fungal biomarkers for the bulk soil, and the FunGuild predicted a higher relative abundance of pathogenic fungi in bulk soil compared to rhizosphere soil. The pH, ammonium nitrogen (NH4+-N), nitrate nitrogen (NO3--N), and total carbon (TC) contents drove microbial community structure and composition. The bacterial network was simpler in the rhizosphere soil than in the bulk soil. However, fungi showed the opposite network pattern. Keystone species in bacterial and fungal networks were mostly involved in nutrient cycling and the C cycling, and were found to be enriched in the rhizosphere soil. Overall, in terms of bacterial and fungal communities, the rhizosphere soil behaves more healthily than the bulk soil and has a higher potential for nutrient cycling.

Anthropogenic Intensity-Determined Assembly and Network Stability of Bacterioplankton Communities in the Le'an River

Bacterioplankton are essential components of riverine ecosystems. However, the mechanisms (deterministic or stochastic processes) and co-occurrence networks by which these communities respond to anthropogenic disturbances are not well understood. Here, we integrated niche-neutrality dynamic balancing and co-occurrence network analysis to investigate the dispersal dynamics of bacterioplankton communities along human activity intensity gradients. Results showed that the lower reaches (where intensity of human activity is high) had an increased composition of bacterioplankton communities which induced strong increases in bacterioplankton diversity. Human activity intensity changes influenced bacterioplankton community assembly via regulation of the deterministic-stochastic balance, with deterministic processes more important as human activity increases. Bacterioplankton molecular ecological network stability and robustness were higher on average in the upper reaches (where there is lower intensity of human activity), but a human activity intensity increase of about 10%/10% can reduce co-occurrence network stability of bacterioplankton communities by an average of 0.62%/0.42% in the dry and wet season, respectively. In addition, water chemistry (especially NO₃^–-N and Cl^–) contributed more to explaining community assembly (especially the composition) than geographic distance and land use in the dry season, while the bacterioplankton community (especially the bacterioplankton network) was more influenced by distance (especially the length of rivers and dendritic streams) and land use (especially forest regions) in the wet season. Our research provides a new perspective of community assembly in rivers and important insights into future research on environmental monitoring and classified management of aquatic ecosystems under the influence of human activity.