Strength of species interactions determines biodiversity and stability in microbial communities

The impact of different rotation regime on the soil bacterial and fungal communities in an intensively managed agricultural region

The continuous wheat-maize planting has led to the increase in epidemic frequency of wheat diseases under climate change. Analyzation of the soil microbial composition in different rotation crops is essential to select alternative rotation regime. This study investigated the bacterial and fungal community abundance and composition, and potential microbe-microbe interactions in three rotations, including wheat-maize → spring maize (WMFS), wheat-soybean (WS) and continuous wheat-maize (WM) planting. The results revealed that there were 110, 156, and 195 bacterial, and 17, 8, and 15 fungal operational taxonomic units respectively enriched by WMFS, WS, and WM. WM increased the relative abundance of Actinobacteria and α-Proteobacteria in wheat, and the relative abundance and copy number of genus Fusarium in maize. WMFS and WS could decrease the abundance of Fusarium in summer-crop across the growth stages and in wheat at elongation. WS also increased the copy number of ammonia-oxidizing bacteria in wheat at flowering and harvest. Network analysis revealed that WM resulted in simple and isolated wheat network with small modules dominating and none Nitrospirae and β-Proteobacteria in the main modules. WS formed interconnected and intricate wheat network with the maximum number of large modules and module connectors. Under WS, positive correlation between antagonistic Streptomyces (Actinobacteria) and genus Fusarium was found in wheat. Soil physicochemical properties explained the majority of the variation in bacterial and fungal β-diversity in wheat (P < 0.01). Rotation regime switching from WM to WMFS and WS may effectively damp the risk of wheat disease and maintain the wheat yield in intensive cereal production.

Scale-Dependent Effects of Growth Stage and Elevational Gradient on Rice Phyllosphere Bacterial and Fungal Microbial Patterns in the Terrace Field

The variation of phyllosphere bacterial and fungal communities along elevation gradients may provide a potential link with temperature, which corresponds to an elevation over short geographic distances. At the same time, the plant growth stage is also an important factor affecting phyllosphere microorganisms. Understanding microbiological diversity over changes in elevation and among plant growth stages is important for developing crop growth ecological theories. Thus, we investigated variations in the composition of the rice phyllosphere bacterial and fungal communities at five sites along an elevation gradient from 580 to 980 m above sea level (asl) in the Ziquejie Mountain at the seedling, heading, and mature stages, using high-throughput Illumina sequencing methods. The results revealed that the dominant bacterial phyla were Proteobacteria, Actinobacteria, and Bacteroidetes, and the dominant fungal phyla were Ascomycota and Basidiomycota, which varied significantly at different elevation sites and growth stages. Elevation had a greater effect on the α diversity of phyllosphere bacteria than on that phyllosphere fungi. Meanwhile, the growth stage had a great effect on the α diversity of both phyllosphere bacteria and fungi. Our results also showed that the composition of bacterial and fungal communities varied significantly along elevation within the different growth stages, in terms of both changes in the relative abundance of species, and that the variations in bacterial and fungal composition were well correlated with variations in the average elevation. A total of 18 bacterial and 24 fungal genera were significantly correlated with elevational gradient, displaying large differences at the various growth stages. Soluble protein (SP) shared a strong positive correlation with bacterial and fungal communities (p < 0.05) and had a strong significant negative correlation with Serratia, Passalora, unclassified_Trichosphaeriales, and antioxidant enzymes (R > 0.5, p < 0.05), and significant positive correlation with the fungal genera Xylaria, Gibberella, and Penicillium (R > 0.5, p < 0.05). Therefore, it suggests that elevation and growth stage might alter both the diversity and abundance of phyllosphere bacterial and fungal populations.

Brenneria goodwinii growth in vitro is improved by competitive interactions with other bacterial species associated with Acute Oak Decline

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Mutually competitive interactions prevail in pairwise cultures of AOD bacteria.

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In vitro growth of brenneria goodwinii is improved by bacterial competition.

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Co-culturing of AOD bacteria indicates evolving improved fitness of B. goodwinii.

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B. goodwinii and R. victoriana can collaborate in vitro to outcompete G. quercinecans.

Brenneria goodwinii, Rahnella victoriana and Gibbsiella quercinecans are three bacterial species frequently isolated together from oak displaying symptoms of Acute Oak Decline (AOD), which include weeping patches on trunks. All three bacterial species play a role in lesion formation in the current episode of AOD in Britain, although B. goodwinii is the most dominant. The ongoing research into stem lesion formation characteristic of this polybacterial syndrome has been focussed primarily on the pathogenicity, identification and taxonomy of these bacteria. As all three species were newly classified within the past ten years, there are many unanswered questions regarding their ecology and interactions with each other. To determine the effect of bacterial interactions on fitness in vitro, we examined pairwise (diculture) and multispecies (triculture) interactions between B. goodwinii, R. victoriana and G. quercinecans in oak leaf media microcosms. Additionally, the effect of co-culturing on the evolution of these species was determined and the evolved B. goodwinii strains were examined further by whole genome sequencing. Our results indicate that B. goodwinii thrived in monoculture with significantly higher viable cell counts than the other two species. Additionally, B. goodwinii performed well in pairwise culture with mutually competitive interactions observed between B. goodwinii and R. victoriana, and between B. goodwinii and G. quercinecans. In the multispecies triculture, B. goodwinii and R. victoriana appeared to exhibit co-ordinated behaviour to outcompete G. quercinecans. After four weeks B. goodwinii grown in co-culture with the other two species developed greater evolved fitness than the strain grown in monoculture as reflected by the increased viable cell counts. The competitive interactions taking place between the threes species indicated evolving improved fitness of B. goodwinii in vitro, that gave it a growth advantage over both R. victoriana and G. quercinecans which showed no significant changes in fitness. Overall, B. goodwinii gains greater benefit in terms of fitness from in vitro competitive interaction with the other two species.

Nutrient supply controls the linkage between species abundance and ecological interactions in marine bacterial communities

Nutrient scarcity is pervasive for natural microbial communities, affecting species reproduction and co-existence. However, it remains unclear whether there are general rules of how microbial species abundances are shaped by biotic and abiotic factors. Here we show that the ribosomal RNA gene operon (rrn) copy number, a genomic trait related to bacterial growth rate and nutrient demand, decreases from the abundant to the rare biosphere in the nutrient-rich coastal sediment but exhibits the opposite pattern in the nutrient-scarce pelagic zone of the global ocean. Both patterns are underlain by positive correlations between community-level rrn copy number and nutrients. Furthermore, inter-species co-exclusion inferred by negative network associations is observed more in coastal sediment than in ocean water samples. Nutrient manipulation experiments yield effects of nutrient availability on rrn copy numbers and network associations that are consistent with our field observations. Based on these results, we propose a “hunger games” hypothesis to define microbial species abundance rules using the rrn copy number, ecological interaction, and nutrient availability.

Environmental and biotic factors control ecological communities. Here, the authors study community ribosomal rRNA gene copy number in coastal sediment and ocean bacterial communities, and in microcosm nutrient addition experiments, to propose a conceptual framework of how nutrient supply and ecological interactions shape the community.

Convergency and Stability Responses of Bacterial Communities to Salinization in Arid and Semiarid Areas: Implications for Global Climate Change in Lake Ecosystems

Climate change has given rise to salinization and nutrient enrichment in lake ecosystems of arid and semiarid areas, which have posed the bacterial communities not only into an ecotone in lake ecosystems but also into an assemblage of its own unique biomes. However, responses of bacterial communities to climate-related salinization and nutrient enrichment remain unclear. In September 2019, this study scrutinized the turnover of bacterial communities along gradients of increasing salinity and nutrient by a space-for-time substitution in Xinjiang Uyghur Autonomous Region, China. We find that salinization rather than nutrient enrichment primarily alters bacterial communities. The homogenous selection of salinization leads to convergent response of bacterial communities, which is revealed by the combination of a decreasing β-nearest taxon index (βNTI) and a pronounced negative correlation between niche breadth and salinity. Furthermore, interspecific interactions within bacterial communities significantly differed among distinct salinity levels. Specifically, mutualistic interactions showed an increase along the salinization. In contrast, topological parameters show hump-shaped curves (average degree and density) and sunken curves (modularity, density, and average path distance), the extremums of which all appear in the high-brackish environment, hinting that bacterial communities are comparatively stable at freshwater and brine environments but are unstable in moderately high-brackish lake.

High-order correlations in species interactions lead to complex diversity-stability relationships for ecosystems

How ecosystems maintain stability is an active area of research. Inspired by applications of random matrix theory in nuclear physics, May showed decades ago that in an ecosystem model with many randomly interacting species, increasing species diversity decreases the stability of the ecosystem. There have since been many additions to May's efforts, one being an improved understanding the effect of mutualistic, competitive, or predator-prey-like correlations between pairs of species. Here we extend a random matrix technique developed in the context of spin-glass theory to study the effect of high-order correlations among species interactions. The resulting analytically solvable models include next-to-nearest-neighbor correlations in the species interaction network, such as the enemy of my enemy is my friend, as well as higher-order correlations. We find qualitative differences from May and others' models, including nonmonotonic diversity-stability relationships. Furthermore, inclusion of particular next-to-nearest-neighbor correlations in predator-prey as opposed to mutualist-competitive networks causes the former to transition to being more stable at higher species diversity. We discuss potential applicability of our results to microbiota engineering and to the ecology of interpredator interactions, such as cub predation between lions and hyenas as well as companionship between humans and dogs.

Characteristics of fungal communities and the sources of mold contamination in mildewed tobacco leaves stored under different climatic conditions

Tobacco mildew is a common postharvest problem caused by fungal growth. It can directly decrease product quality and cause serious economic loss in the tobacco industry. However, the fungal community characteristics of mildewed tobacco leaves and the related influencing factors remain unknown. Here, next-generation sequencing was used to characterize the fungal communities present in mildewed and healthy tobacco leaves stored under three different climatic conditions. Mildewed leaves showed a higher pH and total nitrogen content as well as a lower carbon nitrogen ratio than healthy leaves. Fungal diversity and richness were significantly lower in the mildewed tobacco leaves than in healthy tobacco leaves, with saprophytic fungi such as Xeromyces, Aspergillus, and Wallemia being the dominant molds. Network analysis showed that the complexity, connectivity, and stability of the fungal network were significantly poorer in heavy mildew tobacco leaves than in healthy leaves. NMDS and PERMANOVA analysis showed that the distribution of fungal communities in warehoused tobacco leaves differed significantly across different regions, and temperature and humidity were the key factors affecting these differences. Mildew-causing fungi were significantly enriched in tobacco leaf samples collected in the period between the completion of flue-curing and the start of pre-re-curing. This study demonstrated that mildew is an irreversible process that destroys the balance of the tobacco ecosystem, and that environmental factors play important roles in shaping fungal communities in tobacco leaves.Key points• The diversity and composition of the fungal communities in mildewed tobacco leaves were significantly different from those in healthy tobacco leaves.• Climatic factors may play an important role in shaping fungal communities in tobacco leaves.• Tobacco leaves were most vulnerable to mold contamination between the post-flue-curing and pre-re-curing period.

Soil bacterial diversity and functionality are driven by plant species for enhancing polycyclic aromatic hydrocarbons dissipation in soils

Plant-microorganisms symbiosis has been widely used in developing strategies for the rhizoremediation of polycyclic aromatic hydrocarbon (PAHs) contaminated agricultural soils. However, understanding the potential mechanisms for using complex plant-microbe interactions to enhance rhizoremediation in contaminated soils is still limited. In this study, rhizosphere microbiomes were established by cultivating four types of cover crops for 15 months in a PAHs-contaminated field. The results showed that the PAHs removal rates were significantly higher in rhizosphere soils (55.2-82.3%) than the bare soils (20.5%). Of the four cover crops, the rhizosphere soils associated with the alfalfa and clover had higher removal rates for high molecular weight (HMW) PAHs (78.5-87.1%) than the grasses (39.0-46.2%). High-throughput sequencing analysis showed that bacterial community structure between the planted and bare soils, and among four cover crops rhizosphere soils were significantly different. The rhizosphere soils associated with the alfalfa and clover had more abundant degradation-related taxa. Correlation network analysis showed that bacterial communities with high removal rates have stronger interactions. Metagenome analysis indicated that the relative abundance of the key functional genes involved in PAHs degradation and nutrient metabolisms were significantly higher in rhizosphere soils, especially for alfalfa and clover. Overall, this study provides new insights for us to understand the mechanisms by different plants enhancing PAHs dissipation from the viewpoint of microbiology.

Complementary resource preferences spontaneously emerge in diauxic microbial communities

Many microbes grow diauxically, utilizing the available resources one at a time rather than simultaneously. The properties of communities of microbes growing diauxically remain poorly understood, largely due to a lack of theory and models of such communities. Here, we develop and study a minimal model of diauxic microbial communities assembling in a serially diluted culture. We find that unlike co-utilizing communities, diauxic community assembly repeatably and spontaneously leads to communities with complementary resource preferences, namely communities where species prefer different resources as their top choice. Simulations and theory explain that the emergence of complementarity is driven by the disproportionate contribution of the top choice resource to the growth of a diauxic species. Additionally, we develop a geometric approach for analyzing serially diluted communities, with or without diauxie, which intuitively explains several additional emergent community properties, such as the apparent lack of species which grow fastest on a resource other than their most preferred resource. Overall, our work provides testable predictions for the assembly of natural as well as synthetic communities of diauxically shifting microbes.

Role of FRG1 in predicting the overall survivability in cancers using multivariate based optimal model

FRG1 has a role in tumorigenesis and angiogenesis. Our preliminary analysis showed that FRG1 mRNA expression is associated with overall survival (OS) in certain cancers, but the effect varies. In cervix and gastric cancers, we found a clear difference in the OS between the low and high FRG1 mRNA expression groups, but the difference was not prominent in breast, lung, and liver cancers. We hypothesized that FRG1 expression level could affect the functionality of the correlated genes or vice versa, which might mask the effect of a single gene on the OS analysis in cancer patients. We used the multivariate Cox regression, risk score, and Kaplan Meier analyses to determine OS in a multigene model. STRING, Cytoscape, HIPPIE, Gene Ontology, and DAVID (KEGG) were used to deduce FRG1 associated pathways. In breast, lung, and liver cancers, we found a distinct difference in the OS between the low and high FRG1 mRNA expression groups in the multigene model, suggesting an independent role of FRG1 in survival. Risk scores were calculated based upon regression coefficients in the multigene model. Low and high-risk score groups showed a significant difference in the FRG1 mRNA expression level and OS. HPF1, RPL34, and EXOSC9 were the most common genes present in FRG1 associated pathways across the cancer types. Validation of the effect of FRG1 mRNA expression level on these genes by qRT-PCR supports that FRG1 might be an upstream regulator of their expression. These genes may have multiple regulators, which also affect their expression, leading to the masking effect in the survival analysis. In conclusion, our study highlights the role of FRG1 in the survivability of cancer patients in tissue-specific manner and the use of multigene models in prognosis.

Phage strategies facilitate bacterial coexistence under environmental variability

Bacterial communities are often exposed to temporal variations in resource availability, which exceed bacterial generation times and thereby affect bacterial coexistence. Bacterial population dynamics are also shaped by bacteriophages, which are a main cause of bacterial mortality. Several strategies are proposed in the literature to describe infections by phages, such as "Killing the Winner", "Piggyback the loser" (PtL) or "Piggyback the Winner" (PtW). The two temperate phage strategies PtL and PtW are defined by a change from lytic to lysogenic infection when the host density changes, from high to low or from low to high, respectively. To date, the occurrence of different phage strategies and their response to environmental variability is poorly understood. In our study, we developed a microbial trophic network model using ordinary differential equations (ODEs) and performed 'in silico' experiments. To model the switch from the lysogenic to the lytic cycle, we modified the lysis rate of infected bacteria and their growth was turned on or off using a density-dependent switching point. We addressed whether and how the different phage strategies facilitate bacteria coexistence competing for limiting resources. We also studied the impact of a fluctuating resource inflow to evaluate the response of the different phage strategies to environmental variability. Our results show that the viral shunt (i.e. nutrient release after bacterial lysis) leads to an enrichment of the system. This enrichment enables bacterial coexistence at lower resource concentrations. We were able to show that an established, purely lytic model leads to stable bacterial coexistence despite fluctuating resources. Both temperate phage models differ in their coexistence patterns. The model of PtW yields stable bacterial coexistence at a limited range of resource supply and is most sensitive to resource fluctuations. Interestingly, the purely lytic phage strategy and PtW both result in stable bacteria coexistence at oligotrophic conditions. The PtL model facilitates stable bacterial coexistence over a large range of stable and fluctuating resource inflow. An increase in bacterial growth rate results in a higher resilience to resource variability for the PtL and the lytic infection model. We propose that both temperate phage strategies represent different mechanisms of phages coping with environmental variability. Our study demonstrates how phage strategies can maintain bacterial coexistence in constant and fluctuating environments.

Chicken gut microbiome members limit the spread of an antimicrobial resistance plasmid in Escherichia coli

Plasmid-mediated antimicrobial resistance is a major contributor to the spread of resistance genes within bacterial communities. Successful plasmid spread depends upon a balance between plasmid fitness effects on the host and rates of horizontal transmission. While these key parameters are readily quantified in vitro, the influence of interactions with other microbiome members is largely unknown. Here, we investigated the influence of three genera of lactic acid bacteria (LAB) derived from the chicken gastrointestinal microbiome on the spread of an epidemic narrow-range ESBL resistance plasmid, IncI1 carrying blaCTX-M-1, in mixed cultures of isogenic Escherichia coli strains. Secreted products of LAB decreased E. coli growth rates in a genus-specific manner but did not affect plasmid transfer rates. Importantly, we quantified plasmid transfer rates by controlling for density-dependent mating opportunities. Parametrization of a mathematical model with our in vitro estimates illustrated that small fitness costs of plasmid carriage may tip the balance towards plasmid loss under growth conditions in the gastrointestinal tract. This work shows that microbial interactions can influence plasmid success and provides an experimental-theoretical framework for further study of plasmid transfer in a microbiome context.

The chosen few-variations in common and rare soil bacteria across biomes

Soil bacterial communities are dominated by a few abundant species, while their richness is associated with rare species with largely unknown ecological roles and biogeography. Analyses of previously published soil bacterial community data using a novel classification of common and rare bacteria indicate that only 0.4% of bacterial species can be considered common and are prevalent across biomes. The remaining bacterial species designated as rare are endemic with low relative abundances. Observations coupled with mechanistic models highlight the central role of soil wetness in shaping bacterial rarity. An individual-based model reveals systematic shifts in community composition induced by low carbon inputs in drier soils that deprive common species of exhibiting physiological advantages relative to other species. We find that only a "chosen few" common species shape bacterial communities across biomes; however, their contributions are curtailed in resource-limited environments where a larger number of rare species constitutes the soil microbiome.

Competition dynamics in long-term propagations of Schizosaccharomyces pombe strain communities

Experimental evolution studies with microorganisms such as bacteria and yeast have been an increasingly important and powerful tool to draw long-term inferences of how microbes interact. However, while several strains of the same species often exist in natural environments, many ecology and evolution studies in microbes are typically performed with isogenic populations of bacteria or yeast. In the present study, we firstly perform a genotypic and phenotypic characterization of two laboratory and eight natural strains of the yeast Schizosaccharomyces pombe. We then propagated, in a rich resource environment, yeast communities of 2, 3, 4, and 5 strains for hundreds of generations and asked which fitness-related phenotypes-maximum growth rate or relative competitive fitness-would better predict the outcome of a focal strain during the propagations. While the strain's growth rates would wrongly predict long-term coexistence, pairwise competitive fitness with a focal strain qualitatively predicted the success or extinction of the focal strain by a simple multigenotype population genetics model, given the initial community composition. Interestingly, we have also measured the competitive fitness of the ancestral and evolved communities by the end of the experiment (≈370 generations) and observed frequent maladaptation to the abiotic environment in communities with more than three members. Overall, our results aid establishing pairwise competitive fitness as good qualitative measurement of long-term community composition but also reveal a complex adaptive scenario when trying to predict the evolutionary outcome of those communities.

Insight into the influence of biochar on nitrification based on multi-level and multi-aspect analyses of ammonia-oxidizing microorganisms during cattle manure composting

In this study, influence of biochar on nitrification was explored using multi-level (DNA, RNA, protein) and multi-aspect (diversity, structure, key community, co-occurrence pattern and functional modules) analyses (M-LAA) of ammonia-oxidizing microorganisms (AOMs) during cattle manure composting. Biochar addition increased the copy numbers and diversity of AOMs, restricted (36.02%) the amoA gene transcripts of archaea but increased (24.53%) those of bacteria, and reduced (75.86%) ammonooxygenase (AMO) activity. Crenarchaeota and Thaumarcheota mediated NH₄⁺-N, Unclassified_k_norank_d_Archaea and Crenarchaeota regulated AMO activity and potential ammonia oxidation (PAO) rates. Nitrosomonas and Nitrosospira were the predominant microbial taxa influencing NH₄⁺-N variation and PAO rates, respectively. Additionally, both Crenarchaeota and Nitrosospira played crucial roles in mediating NO₃^--N and NO₂^--N. Furthermore, biochar altered the network patterns of AOMs community by changing the keystone species and the interactivity among communities. These findings indicated that influence of biochar on nitrification could be better explained using M-LAA of AOMs.

Does biological rhythm transmit from plants to rhizosphere microbes?

Plant physiological and metabolic processes are modulated by rhythmic gene expression in a large part. Meanwhile, plants are also regulated by rhizosphere microorganisms, which are fed by root exudates and provide beneficial functions to their plant host. Whether the biorhythms in plants would transfer to the rhizosphere microbial community is still uncertain and their intricate connection remains poorly understood. Here, we investigated the role of the Arabidopsis circadian clock in shaping the rhizosphere microbial community using wild-type plants and clock mutants (cca1-1 and toc1-101) with transcriptomic, metabolomic and 16S rRNA gene sequencing analysis throughout a 24-h period. Deficiencies of the central circadian clock led to abnormal diurnal rhythms for thousands of expressed genes and dozens of root exudates. The bacterial community failed to follow obvious patterns in the 24-h period, and there was lack of coordination with plant growth in the clock mutants. Our results suggest that the robust rhythmicity of genes and root exudation due to circadian clock in plants is an important driving force for the positive succession of rhizosphere communities, which will feedback on plant development.

Insight into the role of extracellular polymeric substances in denitrifying biofilms under nitrobenzene exposure

Denitrifying biofilm promises to be very useful for remediation of nitro-aromatic compounds (NACs) and nitrates in wastewater. Little is known about the role of extracellular polymeric substances (EPS) in nitrobenzene (NB, a typical NAC) remediation, despite the indispensability of EPS for biofilm formation. Herein, the significance of the mechanistic role of EPS in the response of denitrifying biofilms to various levels of NB was investigated. The removal of NB was predominantly controlled via absorption, with little biodegradation during the short-term exposure. Specifically, NB was adsorbed by EPS, as shown by a total adsorption of 40.06% at the initial step, which declined to around 10.52% in the equilibrium stage, while sorption via cells gradually increased from 59.93% to 89.47% over the same period. The results suggested that EPS might act as an important reservoir for NB, which endows inner cells with increased adsorption ability. The presence of EPS might also alleviate the negative impacts of NB toxicity on inner cells, thus protecting microorganisms. This was indicated by the difference in denitrification performance and cell integrity between intact and EPS-free biofilms. High-throughput sequencing data demonstrated that EPS could maintain the stability of microbial communities under NB stress. The fluorescence quenching analysis further indicated that EPS formed stable complexes with NB mainly through hydrophobic interactions with protein-like fractions (tryptophan and tyrosine). Moreover, Fourier transform infrared spectroscopy identified that the hydroxyl, amino, carboxyl, and phosphate groups of EPS were the candidate functional groups binding with NB. Protein secondary structures were also significantly affected, resulting in a loose structure and enhanced hydrophobic performance for EPS. These results provide insights into the role of EPS in alleviating NB-caused cellular stress and the underlying binding mechanisms between NB and EPS.

Resource-diversity relationships in bacterial communities reflect the network structure of microbial metabolism

The relationship between the number of available nutrients and community diversity is a central question in ecological research that remains unanswered. Here we studied the assembly of hundreds of soil-derived microbial communities on a wide range of well-defined resource environments, from single carbon sources to combinations of up to 16. We found that, while single resources supported multispecies communities varying from 8 to 40 taxa, mean community richness increased only one-by-one with additional resources. Cross-feeding could reconcile these seemingly contrasting observations, with the metabolic network seeded by the supplied resources explaining the changes in richness due to both the identity and the number of resources, as well as the distribution of taxa across different communities. By using a consumer-resource model incorporating the inferred cross-feeding network, we provide further theoretical support to our observations and a framework to link the type and number of environmental resources to microbial community diversity.

Identifying driving factors of humic acid formation during rice straw composting based on Fenton pretreatment with bacterial inoculation

The aims of this study were to identify the driving factors of humic acid (HA) during rice straw composting based on Fenton pretreatment with bacterial inoculation. Rice straw was pretreated by Fenton reactions and then inoculated during composting, which was set up CK (control), FeW (Fenton pretreatment) and FeWI (Fenton pretreatment + functional bacterial agents). Results indicated that Fenton pretreatment and inoculation of functional bacteria increased the concentration of HA components, which was due to that bacterial composition was changed and bacterial diversity was decreased. Moreover, Fenton pretreatment and inoculation of functional bacteria increased the bacterial amounts of shikimic acid metabolism genes and the correlation between HA components and shikimic acid metabolism genes. Therefore, the functional bacteria were core driving factors, and NH₄^--N, pH, cellulose and bacterial diversity as key environmental factors to promote the formation of HA components.

Exclusion of the fittest predicts microbial community diversity in fluctuating environments

Microorganisms live in environments that inevitably fluctuate between mild and harsh conditions. As harsh conditions may cause extinctions, the rate at which fluctuations occur can shape microbial communities and their diversity, but we still lack an intuition on how. Here, we build a mathematical model describing two microbial species living in an environment where substrate supplies randomly switch between abundant and scarce. We then vary the rate of switching as well as different properties of the interacting species, and measure the probability of the weaker species driving the stronger one extinct. We find that this probability increases with the strength of demographic noise under harsh conditions and peaks at either low, high, or intermediate switching rates depending on both species' ability to withstand the harsh environment. This complex relationship shows why finding patterns between environmental fluctuations and diversity has historically been difficult. In parameter ranges where the fittest species was most likely to be excluded, however, the beta diversity in larger communities also peaked. In sum, how environmental fluctuations affect interactions between a few species pairs predicts their effect on the beta diversity of the whole community.

Role of Bacillus inoculation in rice straw composting and bacterial community stability after inoculation: Unite resistance or individual collapse

Bacillus is the classic inoculant in rice straw composting. However, there has been no in-depth study of the mechanism promoting the degradation of lignocellulose and the change of indigenous bacterial communities after Bacillus inoculation. Moreover, the stability of bacterial communities is a significant challenge in achieving the efficacy of inoculation. In this study, the ecological succession and yield-resource acquisition-stress tolerance (Y-A-S) framework were combined with Redundancy analysis (RDA) and changes in relative abundance, Bacillus was found to be a pioneer bacterium that adopts a resource acquisition-stress tolerance strategy. The structural equation model (SEM) revealed that in addition to exerting a degradation effect, Bacillus inoculation could also indirectly affect lignocellulose degradation by changing the bacterial community. Random forest model and network analysis indicated a change in bacterial communities after inoculation, and bacteria with more complex relationships and weaker decomposition ability were key to the stability of bacterial communities.

Contribution of single-cell omics to microbial ecology

Micro-organisms play key roles in various ecosystems, but many of their functions and interactions remain undefined. To investigate the ecological relevance of microbial communities, new molecular tools are being developed. Among them, single-cell omics assessing genetic diversity at the population and community levels and linking each individual cell to its functions is gaining interest in microbial ecology. By giving access to a wider range of ecological scales (from individual to community) than culture-based approaches and meta-omics, single-cell omics can contribute not only to micro-organisms' genomic and functional identification but also to the testing of concepts in ecology. Here, we discuss the contribution of single-cell omics to possible breakthroughs in concepts and knowledge on microbial ecosystems and ecoevolutionary processes.

Leveraging Experimental Strategies to Capture Different Dimensions of Microbial Interactions

Microorganisms are a fundamental part of virtually every ecosystem on earth. Understanding how collectively they interact, assemble, and function as communities has become a prevalent topic both in fundamental and applied research. Owing to multiple advances in technology, answering questions at the microbial system or network level is now within our grasp. To map and characterize microbial interaction networks, numerous computational approaches have been developed; however, experimentally validating microbial interactions is no trivial task. Microbial interactions are context-dependent, and their complex nature can result in an array of outcomes, not only in terms of fitness or growth, but also in other relevant functions and phenotypes. Thus, approaches to experimentally capture microbial interactions involve a combination of culture methods and phenotypic or functional characterization methods. Here, through our perspective of food microbiologists, we highlight the breadth of innovative and promising experimental strategies for their potential to capture the different dimensions of microbial interactions and their high-throughput application to answer the question; are microbial interaction patterns or network architecture similar along different contextual scales? We further discuss the experimental approaches used to build various types of networks and study their architecture in the context of cell biology and how they translate at the level of microbial ecosystem.

Compositional Shift of Bacterial, Archaeal, and Fungal Communities Is Dependent on Trophic Lifestyles in Rice Paddy Soil

The soil environment determines plants’ health and performance during their life cycle. Therefore, ecological understanding on variations in soil environments, including physical, chemical, and biological properties, is crucial for managing agricultural fields. Here, we present a comprehensive and extensive blueprint of the bacterial, archaeal, and fungal communities in rice paddy soils with differing soil types and chemical properties. We discovered that natural variations of soil nutrients are important factors shaping microbial diversity. The responses of microbial diversity to soil nutrients were related to the distribution of microbial trophic lifestyles (oligotrophy and copiotrophy) in each community. The compositional changes of bacterial and archaeal communities in response to soil nutrients were mainly governed by oligotrophs, whereas copiotrophs were mainly involved in fungal compositional changes. Compositional shift of microbial communities by fertilization is linked to switching of microbial trophic lifestyles. Random forest models demonstrated that depletion of prokaryotic oligotrophs and enrichment of fungal copiotrophs are the dominant responses to fertilization in low-nutrient conditions, whereas enrichment of putative copiotrophs was important in high-nutrient conditions. Network inference also revealed that trophic lifestyle switching appertains to decreases in intra- and inter-kingdom microbial associations, diminished network connectivity, and switching of hub nodes from oligotrophs to copiotrophs. Our work provides ecological insight into how soil nutrient-driven variations in microbial communities affect soil health in modern agricultural systems.

DNA metabarcoding reveals the significant influence of anthropogenic effects on microeukaryotic communities in urban waterbodies

Biological monitoring and assessment are the first and most fundamental steps towards diagnosing ecological or environmental quality. Increasing anthropogenic impact on urban ecosystems has prompted the development of less expensive and more efficient bioassessment approaches. Generally, a morphospecies based approach is effective for plants and large organisms but challenging for the microbial biosphere. To overcome this challenge, we used high-throughput DNA sequencing for predicting anthropogenic effects on microeukaryotic communities in urban waterbodies along a pollution gradient in Wuhan City, central China in summer 2019. Our results indicated that microeukaryotic community structure was distinct between non-urban polluted reservoir and urban polluted waterbodies. The heterogeneity of environmental condition significantly affected the microeukaryotic diversity, community structure, and species interactions. Integrated co-occurring network analysis revealed that the pollution gradient has a significant adverse impact on network complexity and network dissimilarity. These results revealed that the significant variation in anthropogenically-driven environmental condition shaped microeukaryotic communities in urban freshwater ecosystems. Furthermore, we observed that the relative abundance of indicative OTUs were significantly and negatively correlated with pollution level and these indicative OTUs could be used to predict the water quality status with up to 77% success. Thus, our multiple approaches combining 18S rDNA amplicon sequencing, co-occurring network and indicator species analyses suggest that this study gives a novel approach based on microeukaryotic communities to assess and predict the water quality status of urban aquatic environments.

The Sputum Microbiome in Pulmonary Tuberculosis and Its Association With Disease Manifestations: A Cross-Sectional Study

Each day, approximately 27,000 people become ill with tuberculosis (TB), and 4,000 die from this disease. Pulmonary TB is the main clinical form of TB, and affects the lungs with a considerably heterogeneous manifestation among patients. Immunomodulation by an interplay of host-, environment-, and pathogen-associated factors partially explains such heterogeneity. Microbial communities residing in the host's airways have immunomodulatory effects, but it is unclear if the inter-individual variability of these microbial communities is associated with the heterogeneity of pulmonary TB. Here, we investigated this possibility by characterizing the microbial composition in the sputum of 334 TB patients from Tanzania, and by assessing its association with three aspects of disease manifestations: sputum mycobacterial load, severe clinical findings, and chest x-ray (CXR) findings. Compositional data analysis of taxonomic profiles based on 16S-rRNA gene amplicon sequencing and on whole metagenome shotgun sequencing, and graph-based inference of microbial associations revealed that the airway microbiome of TB patients was shaped by inverse relationships between Streptococcus and two anaerobes: Selenomonas and Fusobacterium. Specifically, the strength of these microbial associations was negatively correlated with Faith's phylogenetic diversity (PD) and with the accumulation of transient genera. Furthermore, low body mass index (BMI) determined the association between abnormal CXRs and community diversity and composition. These associations were mediated by increased abundance of Selenomonas and Fusobacterium, relative to the abundance of Streptococcus, in underweight patients with lung parenchymal infiltrates and in comparison to those with normal chest x-rays. And last, the detection of herpesviruses and anelloviruses in sputum microbial assemblage was linked to co-infection with HIV. Given the anaerobic metabolism of Selenomonas and Fusobacterium, and the hypoxic environment of lung infiltrates, our results suggest that in underweight TB patients, lung tissue remodeling toward anaerobic conditions favors the growth of Selenomonas and Fusobacterium at the expense of Streptococcus. These new insights into the interplay among particular members of the airway microbiome, BMI, and lung parenchymal lesions in TB patients, add a new dimension to the long-known association between low BMI and pulmonary TB. Our results also drive attention to the airways virome in the context of HIV-TB coinfection.

Emergent transcriptional adaption facilitates convergent succession within a synthetic community

Taxonomic convergence is common in bacterial communities but its underlying molecular mechanism remains largely unknown. We thus conducted a time-series transcriptional analysis of a convergent two-species synthetic community that grew in a closed broth-culture system. By analyzing the gene expression and monitoring the community structure, we found that gene expression mainly changed in the early stage, whereas community structure significantly changed in the late stage. The significant change of gene expression occurred even at the very beginning, which was designated as "0 h effect", suggesting the effect of species interaction on gene expression was inevitable. Besides, the effect of interaction on gene expression has a "population effect", which means that majority species have greater impact on gene expressions of minority species than vice versa. Furthermore, gene set enrichment analysis revealed that among a total of 63 unique pathways (occupying about 50% of all the metabolic pathways in both species), 40 (63%) were consistently suppressed, 16 (25%) were conditionally expressed, and only 7 (11%) were consistently activated. Overall, they were strictly regulated by both time and initial structures. Therefore, we proposed that microorganism responses and the induced gene expression changes play important roles in the process of community succession.

Microbial interaction promotes desulfurization efficiency under high pH condition

The existence of H₂S in biogas may cause equipment corrosion and considerable SO₂ emission. Commonly used biotrickling filters may cause biogas dilution or generation of explosive mixtures. Compared with biotrickling filters, two-step process such as bioscrubber filters can overcome these shortages. However, its removal efficiency was still limited due to low microbial activity under high pH condition. Here, a bioreactor filter was carried out under pH 9.0. Removal efficiency higher than 99% was achieved under sulfide loading rate reaching 4.24 kg S m^-3d^-1. Results of network and high throughput sequencing showed that Thiobacillus acted as both dominant species (accounting for 75%) and unique kinless hub in this bioreactor. Other bacteria (accounting for 25%) contributed 75% to the network, which implied the intensive interaction between Thiobacillus and others. Sulfide removal ability and pH tolerance of pure bacteria and mixed culture were considered to verify how microbial interaction influenced them. Compared with pure bacteria, mixed culture had better performance under high pH condition, which confirmed that microbial interaction promoted desulfurization efficiency under high pH condition. These results showed that intensive microbial interaction might be the key to enhance sulfide removal efficiency under high pH condition.

Bacteria-driven phthalic acid ester biodegradation: Current status and emerging opportunities

The extensive use of phthalic acid esters (PAEs) has led to their widespread distribution across various environments. As PAEs pose significant threats to human health, it is urgent to develop efficient strategies to eliminate them from environments. Bacteria-driven PAE biodegradation has been considered as an inexpensive yet effective strategy to restore the contaminated environments. Despite great advances in bacterial culturing and sequencing, the inherent complexity of indigenous microbial community hinders us to mechanistically understand in situ PAE biodegradation and efficiently harness the degrading power of bacteria. The synthetic microbial ecology provides us a simple and controllable model system to address this problem. In this review, we focus on the current progress of PAE biodegradation mediated by bacterial isolates and indigenous bacterial communities, and discuss the prospective of synthetic PAE-degrading bacterial communities in PAE biodegradation research. It is anticipated that the theories and approaches of synthetic microbial ecology will revolutionize the study of bacteria-driven PAE biodegradation and provide novel insights for developing effective bioremediation solutions.

Biodegradable dissolved organic carbon shapes bacterial community structures and co-occurrence patterns in large eutrophic Lake Taihu

Interactions between dissolved organic matter (DOM) and bacteria are central in the biogeochemical cycles of aquatic ecosystems; however, the relative importance of biodegradable dissolved organic carbon (BDOC) compared with other environmental variables in structuring the bacterial communities needs further investigation. Here, we investigated bacterial communities, chromophoric DOM (CDOM) characteristics and physico-chemical parameters as well as examined BDOC via bioassay incubations in large eutrophic Lake Taihu, China, to explore the importance of BDOC for shaping bacterial community structures and co-occurrence patterns. We found that the proportion of BDOC (%BDOC) correlated significantly and positively with the DOC concentration and the index of the contribution of recent produced autochthonous CDOM (BIX). %BDOC, further correlated positively with the relative abundance of the tryptophan-like component and negatively with CDOM aromaticity, indicating that autochthonous production of protein-like CDOM was an important source of BDOC. The richness of the bacterial communities correlated negatively with %BDOC, indicating an enhanced number of species in the refractory DOC environments. %BDOC was identified as a significant stronger factor than DOC in shaping bacterial community composition and the co-occurrence network, suggesting that substrate biodegradability is more significant than DOC quantity determining the bacterial communities in a eutrophic lake. Environmental factors explained a larger proportion of the variation in the conditionally rare and abundant subcommunity than for the abundant and the rare bacterial subcommunities. Our findings emphasize the importance of considering bacteria with different abundance patterns and DOC biodegradability when studying the interactions between DOM and bacteria in eutrophic lakes.

Assembly Processes and Co-occurrence Patterns of Abundant and Rare Bacterial Community in the Eastern Indian Ocean

Microbial communities are composed of many rare species and a few abundant species. Considering the disproportionate importance of rare species for ecosystem functioning, it is important to understand the mechanisms structuring the rare and abundant components of a diverse community in response to environmental changes. Here, we used a 16S ribosomal RNA gene sequencing approach to investigate the bacterial community diversity in the Eastern Indian Ocean (EIO) during the monsoon and intermonsoon. We employed a phylogenetic null model and network analysis to evaluate the assembly processes and co-occurrence pattern of the microbial community. We found that higher bacterial diversity was detected in the intermonsoon with high temperature and low Chlorophyll a concentrations and N/P ratios. The balance between ecological deterministic processes and stochastic processes varied with seasons in the EIO. Meanwhile, conditionally rare taxa (CRT) were more likely modulated by variable selection processes than always rare taxa (ART) and abundant taxa (AT) (CRT > ART > AT). By linking assembly process and species co-occurrence, we demonstrated that the microbial co-occurrence associations tended to be higher when deterministic processes (mainly variable selection) were weaker. This negative trend was observed in rare species rather than abundant species. The linkage could enhance our understanding of the underlying mechanisms underpinning the generation and maintenance of microbial community diversity.

Would that it were so simple: Interactions between multiple traits undermine classical single-trait-based predictions of microbial community function and evolution

Understanding how microbial traits affect the evolution and functioning of microbial communities is fundamental for improving the management of harmful microorganisms, while promoting those that are beneficial. Decades of evolutionary ecology research has focused on examining microbial cooperation, diversity, productivity and virulence but with one crucial limitation. The traits under consideration, such as public good production and resistance to antibiotics or predation, are often assumed to act in isolation. Yet, in reality, multiple traits frequently interact, which can lead to unexpected and undesired outcomes for the health of macroorganisms and ecosystem functioning. This is because many predictions generated in a single-trait context aimed at promoting diversity, reducing virulence or controlling antibiotic resistance can fail for systems where multiple traits interact. Here, we provide a much needed discussion and synthesis of the most recent research to reveal the widespread and diverse nature of multi-trait interactions and their consequences for predicting and controlling microbial community dynamics. Importantly, we argue that synthetic microbial communities and multi-trait mathematical models are powerful tools for managing the beneficial and detrimental impacts of microbial communities, such that past mistakes, like those made regarding the stewardship of antimicrobials, are not repeated.

Keystone microbes affect the evolution and ecological coexistence of the community via species/strain specificity

AIM

Microbial communities exhibit different diversity and fluctuations in the ecological functions due to time and environmental migration. Despite a long history of research and a plethora of data, the factors determining the biodiversity and stability of ecosystems is still elusive.

METHODS AND RESULTS

Here, the Chinese Xiaoqu fermentation system was used as a template to explore the mechanism in which the species specificity and strain in the initial phase affect the community structure and metabolites in the subsequent micro-ecosystem. The micro-ecosystem has been applied for hundreds of years, and the main metabolic function can be reproduced and traced.

CONCLUSIONS

The result proved that Rhizopus spp. is a keystone microbe with a species/strain specificity affecting the trophic interaction niche and function of modules in the complex community through glucose. The fungal community was demonstrated to have a high sealing and stability, while the bacterial community was generally found to change the community structure, physiological function, and interaction relationship, producing strains with connector functions to adapt to fluctuations.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study shows that the taxonomic level of key microbial strains can be changed to affect the evolution of coexistence and functional realisation of the community.

Trophic Interactions and the Drivers of Microbial Community Assembly

Despite numerous surveys of gene and species content in heterotrophic microbial communities, such as those found in animal guts, oceans, or soils, it is still unclear whether there are generalizable biological or ecological processes that control their dynamics and function. Here, we review experimental and theoretical advances to argue that networks of trophic interactions, in which the metabolic excretions of one species are the primary resource for another, constitute the central drivers of microbial community assembly. Trophic interactions emerge from the deconstruction of complex forms of organic matter into a wealth of smaller metabolic intermediates, some of which are released to the environment and serve as a nutritional buffet for the community. The structure of the emergent trophic network and the rate at which primary resources are supplied control many features of microbial community assembly, including the relative contributions of competition and cooperation and the emergence of alternative community states. Viewing microbial community assembly through the lens of trophic interactions also has important implications for the spatial dynamics of communities as well as the functional redundancy of taxonomic groups. Given the ubiquity of trophic interactions across environments, they impart a common logic that can enable the development of a more quantitative and predictive microbial community ecology.

Commensal inter-bacterial interactions shaping the microbiota

The gut microbiota, a complex ecosystem of microorganisms of different kingdoms, impacts host physiology and disease. Within this ecosystem, inter-bacterial interactions and their impacts on microbiota community structure and the eukaryotic host remain insufficiently explored. Microbiota-related inter-bacterial interactions range from symbiotic interactions, involving exchange of nutrients, enzymes, and genetic material; competition for nutrients and space, mediated by biophysical alterations and secretion of toxins and anti-microbials; to predation of overpopulating bacteria. Collectively, these understudied interactions hold important clues as to forces shaping microbiota diversity, niche formation, and responses to signals perceived from the host, incoming pathogens and the environment. In this review, we highlight the roles and mechanisms of selected inter-bacterial interactions in the microbiota, and their potential impacts on the host and pathogenic infection. We discuss challenges in mechanistically decoding these complex interactions, and prospects of harnessing them as future targets for rational microbiota modification in a variety of diseases.

Towards a deeper understanding of microbial communities: integrating experimental data with dynamic models

Microbial communities and their functions are shaped by complex networks of interactions among microbes and with their environment. While the critical roles microbial communities play in numerous environments have become increasingly appreciated, we have a very limited understanding of their interactions and how these interactions combine to generate community-level behaviors. This knowledge gap hinders our ability to predict community responses to perturbations and to design interventions that manipulate these communities to our benefit. Dynamic models are promising tools to address these questions. We review existing modeling techniques to construct dynamic models of microbial communities at different scales and suggest ways to leverage multiple types of models and data to facilitate our understanding and engineering of microbial communities.

The spatial organization of microbial communities during range expansion

Microbes in nature often live in dense and diverse communities exhibiting a variety of spatial structures. Microbial range expansion is a universal ecological process that enables populations to form spatial patterns. It can be driven by both passive and active processes, for example, mechanical forces from cell growth and bacterial motility. In this review, we provide a taste of recent creative and sophisticated efforts being made to address basic questions in spatial ecology and pattern formation during range expansion. We especially highlight the role of motility to shape community structures, and discuss the research challenges and future directions.

Application of constructed wetlands in treating rural sewage from source separation with high-influent nitrogen load: a review

Constructed wetlands (CWs) are characterized by low construction cost, convenient maintenance and management, and environmentally friendly features. They have emerged as promising technologies for decentralized sewage treatment across rural areas. Source separation of black water and gray water can facilitate sewage recycling and reuse of reclaimed water, reduce the size of treatment facilities, and lower infrastructure investment and operating cost. This is consistent with the concept of sustainable development. However, black water contains high concentrations of ammonia nitrogen, and the denitrification capacity of CWs is not excellent due to insufficient carbon source. Therefore, application of CWs for black water treatment faces challenges. This article provides a review on the progress in CWs for treatment of the sewage with high-influent nitrogen load, with emphasis on the commonly used strengthening means and the role of plants in nitrogen removal via CWs. The current issues of rural sewage treatment with high-influent nitrogen load by CWs are also assessed. Finally, the challenges and perspectives are discussed for the optimization of CWs-enhanced denitrification strategies.

Soil actinobacteria tend to have neutral interactions with other co-occurring microorganisms, especially under oligotrophic conditions

Actinobacteria produce a variety of secondary metabolites that can influence the survival or behaviour of other organisms. The understanding of the ecological roles of actinobacteria has significantly improved in the past decades, but a systematic insight into the interactions between actinobacteria and other microbes in nature is warranted. Here, we studied the pairwise effects of actinobacteria on other microbes isolated from red soils under different nutritional conditions. We found that neutral effects dominated the interactions, accounting for 68.1% of the interactions in eutrophic conditions and for a significantly higher proportion (86.2%) in oligotrophic conditions. High nutrient levels boosted active metabolism of actinobacteria and generally made them more aggressive, supporting the stress gradient hypothesis. The secondary metabolites produced by actinobacteria played a pivotal role in interference competition with other microbes, of which the role of desferrioxamine siderophores could not be ignored. Niche overlap seemed to be another cause of competition, notably under oligotrophic conditions. Moreover, the large-scale phylogeny had a much greater impact on the interaction than the location origin of the microbes. These results provide an understanding of the coexistence of actinobacteria with other microbes in nature and suggest neutrality as a key mechanism for maintaining microbial diversity in soils.

Nitrogen-cycling gene pool shrunk by species interactions among denser bacterial and archaeal community stimulated by excess organic matter and total nitrogen in a eutrophic bay

Microbial densities, functional genes, and their responses to environment factors have been studied for years, but still a lot remains unknown about their interactions with each other. In this study, the abundances of 7 nitrogen cycling genes in the sediments from Hangzhou Bay were analyzed along with bacterial and archaeal 16S rRNA abundances as the biomarkers of their densities. The amount of organic matter (OM) and total nitrogen (TN) strongly positively correlated with each other and microbial densities, while total phosphate (TP) and ammonia-nitrogen (NH₃-N) did not. Most studied genes were density suppressed, while nirS was density stable, and nosZ and hzo were density irrelevant. This suggests eutrophication could limit inorganic nitrogen cycle pathways and the removal of nitrogen in the sediment and emit more greenhouse gases. This study provides a new insight of microbial community structures, functions and their interactions in the sediments of eutrophic bays.

Interspecies bacterial competition regulates community assembly in the C. elegans intestine

From insects to mammals, a large variety of animals hold in their intestines complex bacterial communities that play an important role in health and disease. To further our understanding of how intestinal bacterial communities assemble and function, we study the C. elegans microbiota with a bottom-up approach by feeding this nematode with bacterial monocultures as well as mixtures of two to eight bacterial species. We find that bacteria colonizing well in monoculture do not always do well in co-cultures due to interspecies bacterial interactions. Moreover, as community diversity increases, the ability to colonize the worm gut in monoculture becomes less important than interspecies interactions for determining community assembly. To explore the role of host-microbe adaptation, we compare bacteria isolated from C. elegans intestines and non-native isolates, and we find that the success of colonization is determined more by a species' taxonomy than by the isolation source. Lastly, by comparing the assembled microbiotas in two C. elegans mutants, we find that innate immunity via the p38 MAPK pathway decreases bacterial abundances yet has little influence on microbiota composition. These results highlight that bacterial interspecies interactions, more so than host-microbe adaptation or gut environmental filtering, play a dominant role in the assembly of the C. elegans microbiota.

Extremophiles in Soil Communities of Former Copper Mining Sites of the East Harz Region (Germany) Reflected by Re-Analyzed 16S rRNA Data

The east and southeast rim of Harz mountains (Germany) are marked by a high density of former copper mining places dating back from the late 20th century to the middle age. A set of 18 soil samples from pre- and early industrial mining places and one sample from an industrial mine dump have been selected for investigation by 16S rRNA and compared with six samples from non-mining areas. Although most of the soil samples from the old mines show pH values around 7, RNA profiling reflects many operational taxonomical units (OTUs) belonging to acidophilic genera. For some of these OTUs, similarities were found with their abundances in the comparative samples, while others show significant differences. In addition to pH-dependent bacteria, thermophilic, psychrophilic, and halophilic types were observed. Among these OTUs, several DNA sequences are related to bacteria which are reported to show the ability to metabolize special substrates. Some OTUs absent in comparative samples from limestone substrates, among them Thaumarchaeota were present in the soil group from ancient mines with pH > 7. In contrast, acidophilic types have been found in a sample from a copper slag deposit, e.g., the polymer degrading bacterium Granulicella and Acidicaldus, which is thermophilic, too. Soil samples of the group of pre-industrial mines supplied some less abundant, interesting OTUs as the polymer-degrading Povalibacter and the halophilic Lewinella and Halobacteriovorax. A particularly high number of bacteria (OTUs) which had not been detected in other samples were found at an industrial copper mine dump, among them many halophilic and psychrophilic types. In summary, the results show that soil samples from the ancient copper mining places contain soil bacterial communities that could be a promising source in the search for microorganisms with valuable metabolic capabilities.

Properties of Equilibria and Glassy Phases of the Random Lotka-Volterra Model with Demographic Noise

We study a reference model in theoretical ecology, the disordered Lotka-Volterra model for ecological communities, in the presence of finite demographic noise. Our theoretical analysis, valid for symmetric interactions, shows that for sufficiently heterogeneous interactions and low demographic noise the system displays a multiple equilibria phase, which we fully characterize. In particular, we show that in this phase the number of locally stable equilibria is exponential in the number of species. Upon further decreasing the demographic noise, we unveil the presence of a second transition like the so-called "Gardner" transition to a marginally stable phase similar to that observed in the jamming of amorphous materials. We confirm and complement our analytical results by numerical simulations. Furthermore, we extend their relevance by showing that they hold for other interacting random dynamical systems such as the random replicant model. Finally, we discuss their extension to the case of asymmetric couplings.

Pulse Frequency in Crop Rotations Alters Soil Microbial Community Networks and the Relative Abundance of Fungal Plant Pathogens

Including pulse crops in cereal-based cropping systems has become a widely accepted and useful agronomic practice to increase crop diversification and biologically fixed nitrogen in agroecosystems. However, there is a lack of knowledge regarding how the intensification of pulses in crop rotations influence soil microbial communities. In this study, we used an amplicon sequencing approach to examine the bulk and rhizosphere soil bacterial and fungal communities from the wheat (Triticum aestivum L.) phase (final year of 4 years rotations) of a long-term pulse intensification field trial in the semi-arid region of the Canadian Prairies. Our results revealed pulse frequency had a minimal impact on microbial α-diversity, but caused a significant shift in the composition of the fungal (rhizosphere and bulk soil) and bacterial (bulk soil) communities. This effect was the most pronounced in the Ascomycete and Bacteroidete communities. Increasing pulse frequency also promoted a higher proportion of fungal pathotrophs in the bulk soil, particularly those putatively identified as plant pathogens. The network analysis revealed that rotations with higher pulse frequency promoted increased competition within the soil microbial networks in the rhizosphere and bulk soil. However, we also detected more negative interactions among the dominant pathotrophic taxa with increased pulse frequency, suggesting higher soil-borne disease potential. These findings highlight the potential drawbacks and reduced sustainability of increasing pulse frequency in crop rotations in semiarid environments.

Detection of functional microorganisms in benzene [a] pyrene-contaminated soils using DNA-SIP technology

DNA-SIP technology was used to detect active BaP-degraders involved in the biodegradation of benzo [a] pyrene (BaP) in two soils separately and in mixture. The lowest BaP removal was observed in red soil, and Ramlibacter (OTU830) belonging to the γ-Proteobacteria was labeled as BaP degrader with ¹³C-BaP. The highest diversity of degrading microorganisms occurred in the paddy soil with OTUs belonging to Nocardioids, Micromonospora, Saccharothrix, Lysobacter and Methylium present and a BaP removal efficiency of 29.5% after 14 d. BaP degraders in the mixed microbiome of the soil mixture were Burkholderia and Phenylobacterium, together with Nocardioides and Micromonospora as in the paddy soil. These results indicated that the active BaP-degraders in the mixed microbiome were identical to the active BaP-degraders in paddy soil (OTU356 and OTU328), but also unique in the mixed microbiome, such as OTU393 and OTU392. The functional genes of PAH-ring hydroxylating dioxygenases (PAH-RHD_α) were expressed and were positively related to the removal of BaP, and the active BaP degrading bacteria included both Gram-positive and Gram-negative bacteria. Saccharothrix, Phylobacterium, Micromonospora and Nocardioids are here reported as BaP degraders for the first time using DNA-SIP.

Response of a methane-driven interaction network to stressor intensification

Microorganisms may reciprocally select for specific interacting partners, forming a network with interdependent relationships. The methanotrophic interaction network, comprising methanotrophs and non-methanotrophs, is thought to modulate methane oxidation and give rise to emergent properties beneficial for the methanotrophs. Therefore, microbial interaction may become relevant for community functioning under stress. However, empirical validation of the role and stressor-induced response of the interaction network remains scarce. Here, we determined the response of a complex methane-driven interaction network to a stepwise increase in NH4Cl-induced stress (0.5-4.75 g L-1, in 0.25-0.5 g L-1 increments) using enrichment of a naturally occurring complex community derived from a paddy soil in laboratory-scale incubations. Although ammonium and intermediates of ammonium oxidation are known to inhibit methane oxidation, methanotrophic activity was unexpectedly detected even in incubations with high ammonium levels, albeit rates were significantly reduced. Sequencing analysis of the 16S rRNA and pmoA genes consistently revealed divergent communities in the reference and stressed incubations. The 16S rRNA-based co-occurrence network analysis revealed that NH4Cl-induced stress intensification resulted in a less complex and modular network, likely driven by less stable interaction. Interestingly, the non-methanotrophs formed the key nodes, and appear to be relevant members of the community. Overall, stressor intensification unravels the interaction network, with adverse consequences for community functioning.