Keystone taxa predict compositional change in microbial communities

Solutions in microbiome engineering: prioritizing barriers to organism establishment

Microbiome engineering is increasingly being employed as a solution to challenges in health, agriculture, and climate. Often manipulation involves inoculation of new microbes designed to improve function into a preexisting microbial community. Despite, increased efforts in microbiome engineering inoculants frequently fail to establish and/or confer long-lasting modifications on ecosystem function. We posit that one underlying cause of these shortfalls is the failure to consider barriers to organism establishment. This is a key challenge and focus of macroecology research, specifically invasion biology and restoration ecology. We adopt a framework from invasion biology that summarizes establishment barriers in three categories: (1) propagule pressure, (2) environmental filtering, and (3) biotic interactions factors. We suggest that biotic interactions is the most neglected factor in microbiome engineering research, and we recommend a number of actions to accelerate engineering solutions.

Natural Recovery from Fire Disturbance is More Favorable than Assisted Recovery for the Restoration of Soil Nematode-trapping Fungi

Fire is usually considered a severe disturbance factor in environment. Globally, rising temperatures and increasing human activities have intensified the severity and frequency of fire incidents; research on postfire recovery has inevitably become an important focus for ecologists. In terms of the restoration of burned areas, there are usually two primary approaches: natural recovery and assisted recovery. However, there are very few relevant studies that systematically compared these recovery alternatives suggesting which one is more favorable to the overall restoration of an ecosystem, especially to the soil microbes that function as indispensable components of ecosystems. In this study, the restoration of soil nematode-trapping fungi (NTF) was compared between natural and assisted recovery environments. Results showed that although the NTF community structures differed among the sample sites, the counts and diversity of the NTF communities in the upper and lower soil layers in the natural recovery area were higher than those in the assisted recovery and the unburned control areas. These findings suggests that artificial efforts to help ecosystem recovery after fire produce negative effects on the speed and quality of soil NTF community recovery. Instead, natural recovery appears to be the more suitable land management choice after fire disturbance.

Anemochore Seeds Harbor Distinct Fungal and Bacterial Abundance, Composition, and Functional Profiles

Many plants adapted to harsh environments have evolved low seed mass ('light seeds') with specific dispersal strategies, primarily either by wind (anemochory) or water (hydrochory). However, the role of their seed microbiota in their survival, and their seed microbial abundance and structure, remain insufficiently studied. Herein, we studied the light seed microbiome of eight anemochores and two hydrochores (as controls) collected from four provinces in China, using qPCR and metagenomic sequencing targeting both bacteria and fungi. Substantial variations were found for seed endophytic fungi (9.9 × 1010~7.3 × 102 gene copy numbers per seed) and bacteria (1.7 × 1010~8.0 × 106). Seed microbial diversity and structure were mainly driven by the plant genotype (species), with weak influences from their host plant classification level or dispersal mode. Seed microbial composition differences were clear at the microbial phylum level, with dominant proportions (~75%) for Proteobacteria and Ascomycota. The light seeds studied harbored unique microbial signatures, sharing only two Halomonas amplicon sequence variants (ASVs) and two fungal ASVs affiliated to Alternaria and Cladosporium. A genome-level functional profile analysis revealed that seed bacterial microbiota were enriched in amino acid, nucleoside, and nucleotide biosynthesis, while in fungal communities the generation of precursor metabolites and respiration were more highly represented. Together, these novel insights provide a deeper understanding of highly diversified plant-specific light seed microbiota and ecological strategies for plants in harsh environments.

The potential role of fertilizer-derived exogenous bacteria on soil bacterial community assemblage and network formation

Manure fertilization contributes to crop production and sustainable agriculture by introducing large amounts of nutrients and exogenous microbes into soil. However, the contribution of exogenous microbes in shaping soil bacterial community and network structure after fertilization are still controversial. In this study, bacterial communities and network structure that received unsterilized (R + C) or sterilized (R + SC) manure fertilizers, as well as no fertilizer control (R), were characterized using high throughput sequencing. Results showed that the relative abundance of fertilizer-derived OTUs decreased from 10.4% to 4.6% after 90 days incubation, while the Bray-Curtis distance between the control and fertilization group (R + C and R + SC) gradually increased with the culture time. It can be supposed that manure fertilization altered soil bacterial communities by interfering the growth of indigenous bacteria rather than the colonization of fertilizer-derived bacteria. Network analysis showed that a subset of the fertilizer-derived OTUs identified as Xanthomonadales order and Promicromonospora, Constrictibacter genera acted as connectors between modules. They enhanced the interactions not only between soil-derived OTUs and fertilizer-derived OTUs, but also within indigenous bacteria, supported that the introduction of fertilizer-derived exogenous bacteria contributes large to soil bacterial network association. Moreover, fertilizer-derived OTUs presented to be positively correlated with soil pH, while majority soil-derived OTUs presented to be negatively correlated with various physicochemical variables (pH, DOC, NO₃^-, and LAP). Our study highlighted the critical role of fertilizer-derived bacteria in regulating indigenous soil microbial community and network formation after fertilization.

Soil Rehabilitation Promotes Resilient Microbiome with Enriched Keystone Taxa than Agricultural Infestation in Barren Soils on the Loess Plateau

Drylands provide crucial ecosystem and economic services across the globe. In barren drylands, keystone taxa drive microbial structure and functioning in soil environments. In the current study, the Chinese Loess plateau’s agricultural (AL) and twenty-year-old rehabilitated lands (RL) provided a unique opportunity to investigate land-use-mediated effects on barren soil keystone bacterial and fungal taxa. Therefore, soils from eighteen sites were collected for metagenomic sequencing of bacteria specific 16S rRNA and fungi specific ITS2 regions, respectively, and to conduct molecular ecological networks and construct microbial OTU-based correlation matrices. In RL soils we found a more complex bacterial network represented by a higher number of nodes and links, with a link percentage of 77%, and a lower number of nodes and links for OTU-based fungal networks compared to the AL soils. A higher number of keystone taxa was observed in the RL (66) than in the AL (49) soils, and microbial network connectivity was positively influenced by soil total nitrogen and microbial biomass carbon contents. Our results indicate that plant restoration and the reduced human interventions in RL soils could guide the development of a better-connected microbial network and ensure sufficient nutrient circulation in barren soils on the Loess plateau.

Inter-phylum negative interactions affect soil bacterial community dynamics and functions during soybean development under long-term nitrogen fertilization

Understanding interspecies interactions is essential to predict the response of microbial communities to exogenous perturbation. Herein, rhizospheric and bulk soils were collected from five developmental stages of soybean, which grew in soils receiving 16-year nitrogen inputs. Bacterial communities and functional profiles were examined using high-throughput sequencing and quantitative PCR, respectively. The objective of this study was to identify the key bacterial interactions that influenced community dynamics and functions. We found that the stages of soybean development outcompeted nitrogen fertilization management in shaping bacterial community structure, while fertilization treatments significantly shaped the abundance distribution of nitrogen functional genes. Temporal variations in bacterial abundances increased in bulk soils, especially at the stage of soybean branching, which helps to infer underlying negative interspecies interactions. Members of Cyanobacteria and Actinobacteria actively engaged in inter-phylum negative interactions in bulk soils and soybean rhizosphere, respectively. Furthermore, the negative interactions between nitrogen-fixing functional groups and the reduction of nifH gene abundance were coupled during soybean development, which may help to explain the linkages between population dynamics and functions. Overall, these findings highlight the importance of inter-phylum negative interactions in shaping the correlation patterns of bacterial communities and in determining soil functional potential.

A Generalist Lifestyle Allows Rare Gardnerella spp. to Persist at Low Levels in the Vaginal Microbiome

Gardnerella spp. are considered a hallmark of bacterial vaginosis, a dysbiosis of the vaginal microbiome. There are four cpn60 sequence-based subgroups within the genus (A, B, C and D), and thirteen genome species have been defined recently. Gardnerella spp. co-occur in the vaginal microbiome with varying abundance, and these patterns are shaped by a resource-dependent, exploitative competition, which affects the growth rate of subgroups A, B and C negatively. The growth rate of rarely abundant subgroup D, however, increases with the increasing number of competitors, negatively affecting the growth rate of others. We hypothesized that a nutritional generalist lifestyle and minimal niche overlap with the other more abundant Gardnerella spp. facilitate the maintenance of subgroup D in the vaginal microbiome through negative frequency-dependent selection. Using 40 whole-genome sequences from isolates representing all four subgroups, we found that they could be distinguished based on the content of their predicted proteomes. Proteins associated with carbohydrate and amino acid uptake and metabolism were significant contributors to the separation of subgroups. Subgroup D isolates had significantly more of their proteins assigned to amino acid metabolism than the other subgroups. Subgroup D isolates were also significantly different from others in terms of number and type of carbon sources utilized in a phenotypic assay, while the other three could not be distinguished. Overall, the results suggest that a generalist lifestyle and lack of niche overlap with other Gardnerella spp. leads to subgroup D being favoured by negative frequency-dependent selection in the vaginal microbiome.

Microbial community profiles in soils adjacent to mining and smelting areas: Contrasting potentially toxic metals and co-occurrence patterns

Mining and smelting activities have introduced severe potentially toxic metals (PTMs) contamination into surrounding soil settings. Influences of PTMs on microbial diversity have been widely studied. However, variations of microbial communities, network structures and community functions in different levels of PTMs contaminated soils adjacent to mining and smelting aera are still poorly investigated. In this study, microbial communities of soils around different levels of PTMs contamination were comprehensively studied by 16S rRNA gene amplicons high-throughput sequencing. Microbial interactions and module functions were also exploited to ascertain the discrepancies of PTMs concentration levels on microbial ecological functions. Results indicated that the microbial community composition was significantly distinct attributed to the phylum Protebacteria (p = 0.002) dominating in soil with high level PTMs contents but Actinobacteria (p = 0.002) in low level of PTMs-contaminated soil. Microbial α diversity was not significantly influenced by different levels of PTMs contaminations. Microorganisms proactively responded to PTMs content levels by means of strengthening network complexities and modularities among microbe-microbe interactions. The functions of main network modules were predicted associating membrane transport, amino acid metabolism, energy metabolism and carbohydrate metabolism. The PTMs detoxification and anti-oxidation were significantly strengthened at the high level of PTMs contamination. The present study demonstrated that modification of microbial community by the adaptive adjustment of microbial compositions and strengthening their network complexity and modularity.

Effects of warming on the bacterial community and its function in a temperate steppe

As a significant environmental issue, global warming will have a significant impact on soil microorganisms, especially soil bacteria. However, the effects of warming on the network structure of bacterial communities and the function of ecosystems remain unclear. Therefore, we examined the effects of three-year simulated field warming on the complexity of soil bacterial communities and predicted functions in a temperate steppe of Inner Mongolia. Warming significantly increased the α-diversity of bacteria in 2018 but did not affect it in 2019 and 2020. Warming increased network complexity and stability and keystone taxa, and these bacterial taxa also associated more closely with each other, indicating that the protection of interactions between bacterial taxa is very important for the conservation of biodiversity. Warming significantly increased aerobic chemoheterotrophy, ureolysis, and chemoheterotrophy, suggesting that warming increased the ability of bacteria to decompose organic matter and the emission of greenhouse gases, such as CO₂ and CH₄. Collectively, warming will alter soil bacterial community structure and its potential functions, further affecting key functions in grassland belowground ecosystems.

Fine-Scale Spatial Structure of Soil Microbial Communities in Burrows of a Keystone Rodent Following Mass Mortality

Soil microbial communities both reflect and influence biotic and abiotic processes occurring at or near the soil surface. Ecosystem engineers that physically alter the soil surface, such as burrowing ground squirrels, are expected to influence the distribution of soil microbial communities. Black-tailed prairie dogs (Cynomys ludovicianus) construct complex burrows in which activities such as nesting, defecating, and dying are partitioned spatially into different chambers. Prairie dogs also experience large-scale die-offs due to sylvatic plague, caused by the bacterium Yersinia pestis, which lead to mass mortality events with potential repercussions on microbial communities. We used 16S sequencing to examine microbial communities in soil that was excavated by prairie dogs from different burrow locations, and surface soil that was used in the construction of burrow entrances, in populations that experienced plague die-offs. Following the QIIME2 pipeline, we assessed microbial diversity at several taxonomic levels among burrow regions. To do so, we computed community similarity metrics (Bray–Curtis, Jaccard, and weighted and unweighted UniFrac) among samples and community diversity indexes (Shannon and Faith phylogenetic diversity indexes) within each sample. Microbial communities differed across burrow regions, and several taxa exhibited spatial variation in relative abundance. Microbial ecological diversity (Shannon index) was highest in soil recently excavated from within burrows and soils associated with dead animals, and was lowest in soils associated with scat. Phylogenetic diversity varied only marginally within burrows, but the trends paralleled those for Shannon diversity. Yersinia was detected in four samples from one colony, marking the first time the genus has been sampled from soil on prairie dog colonies. The presence of Yersinia was a significant predictor of five bacterial families and eight microbial genera, most of which were rare taxa found in higher abundance in the presence of Yersinia, and one of which, Dictyostelium, has been proposed as an enzootic reservoir of Y. pestis. This study demonstrates that mammalian modifications to soil structure by physical alterations and by mass mortality can influence the distribution and diversity of microbial communities.

Elevated pCO2 alters the interaction patterns and functional potentials of rearing seawater microbiota

Mean oceanic CO₂ values have already risen and are expected to rise further on a global scale. Elevated pCO₂ (eCO₂) changes the bacterial community in seawater. However, the ecological association of seawater microbiota and related geochemical functions are largely unknown. We provide the first evidence that eCO₂ alters the interaction patterns and functional potentials of microbiota in rearing seawater of the swimming crab, Portunus trituberculatus. Network analysis showed that eCO₂ induced a simpler and more modular bacterial network in rearing seawater, with increased negative associations and distinct keystone taxa. Using the quantitative microbial element cycling method, nitrogen (N) and phosphorus (P) cycling genes exhibited the highest increase after one week of eCO₂ stress and were significantly associated with keystone taxa. However, the functional potential of seawater bacteria was decoupled from their taxonomic composition and strongly coupled with eCO₂ levels. The changed functional potential of seawater bacteria contributed to seawater N and P chemistry, which was highlighted by markedly decreased NH₃, NH₄⁺-N, and PO₄^3--P levels and increased NO₂^--N and NO₃^--N levels. This study suggests that eCO₂ alters the interaction patterns and functional potentials of seawater microbiota, which lead to the changes of seawater chemical parameters. Our findings provide new insights into the mechanisms underlying the effects of eCO₂ on marine animals from the microbial ecological perspective.

Key microorganisms mediate soil carbon-climate feedbacks in forest ecosystems

Soil microorganisms are known to significantly contribute to climate change through soil carbon (C) cycle feedbacks. However, it is challenging to incorporate these feedbacks into predictions of future patterns of terrestrial C cycling, largely because of the vast diversity of soil microorganisms and their responses to environmental conditions. Here, we show that the composition of the bacterial community can provide information about the microbial community-level thermal response (MCTR), which drives ecosystem-scale soil C-climate feedbacks. The dominant taxa from 169 sites representing a gradient from tropical to boreal forest mainly belonged to the phyla Actinobacteria and Acidobacteria. Moreover, we show that the MCTR in warm biomes and acidic soils was linked primarily to bacteria, whereas the MCTR in cold biomes and alkaline soils was primarily associated with fungi. Our results provide strong empirical evidence of linkages between microbial composition and the MCTR across a wide range of forests, and suggest the importance of specific microorganisms in regulating soil C-climate feedbacks.

Genetic Elucidation of Quorum Sensing and Cobamide Biosynthesis in Divergent Bacterial-Fungal Associations Across the Soil-Mangrove Root Interface

Plant roots in soil host a repertoire of bacteria and fungi, whose ecological interactions could improve their functions and plant performance. However, the potential microbial interactions and underlying mechanisms remain largely unknown across the soil-mangrove root interface. We herein analyzed microbial intra- and inter-domain network topologies, keystone taxa, and interaction-related genes across four compartments (non-rhizosphere, rhizosphere, episphere, and endosphere) from a soil-mangrove root continuum, using amplicon and metagenome sequencing technologies. We found that both intra- and inter-domain networks displayed notable differences in the structure and topology across four compartments. Compared to three peripheral compartments, the endosphere was a distinctive compartment harboring more dense co-occurrences with a higher average connectivity in bacterial-fungal network (2.986) than in bacterial (2.628) or fungal network (2.419), which could be related to three bacterial keystone taxa (Vibrio, Anaerolineae, and Desulfarculaceae) detected in the endosphere as they are known to intensify inter-domain associations with fungi and stimulate biofilm formation. In support of this finding, we also found that the genes involved in cell-cell communications by quorum sensing (rhlI, lasI, pqsH, and lasR) and aerobic cobamide biosynthesis (cobG, cobF, and cobA) were highly enriched in the endosphere, whereas anaerobic cobamide biosynthesis (encoded by cbiT and cbiE) was dominant in three peripheral compartments. Our results provide genetic evidence for the intensified bacterial-fungal associations of root endophytes, highlighting the critical role of the soil-root interface in structuring the microbial inter-domain associations.

Core bacterial community driven the conversion of fulvic acid components during composting with adding manganese dioxide

Here, we revealed the effects of microbes on fulvic acid (FA) formation in composting by adding MnO₂. The results showed that the MnO₂ promoted the formation of highly humified components (79.2% increased for component 2, and 45.8% increased for component 3) in FA. Additionally, core bacteria involved in FA transformation were identified, the MnO₂ increased the relative abundance of core bacteria. Notably, two different core bacteria types were identified: "transforming bacteria" and "processing bacteria". The "transforming bacteria" dominated (about 40% contribution) in the formation of FA components with a high humification degree. The structural equation model confirmed that "transforming bacteria" could convert partly FA components with low humification into highly humified components, and the "transforming bacteria" could be regulated by environmental factors. These findings provided a new insight to manage FA humification degree during composting and helped to improve the application value of FA.

Fungi in Permafrost-Affected Soils of the Canadian Arctic: Horizon- and Site-Specific Keystone Taxa Revealed by Co-Occurrence Network

Permafrost-affected soil stores a significant amount of organic carbon. Identifying the biological constraints of soil organic matter transformation, e.g., the interaction of major soil microbial soil organic matter decomposers, is crucial for predicting carbon vulnerability in permafrost-affected soil. Fungi are important players in the decomposition of soil organic matter and often interact in various mutualistic relationships during this process. We investigated four different soil horizon types (including specific horizons of cryoturbated soil organic matter (cryoOM)) across different types of permafrost-affected soil in the Western Canadian Arctic, determined the composition of fungal communities by sequencing (Illumina MPS) the fungal internal transcribed spacer region, assigned fungal lifestyles, and by determining the co-occurrence of fungal network properties, identified the topological role of keystone fungal taxa. Compositional analysis revealed a significantly higher relative proportion of the litter saprotroph Lachnum and root-associated saprotroph Phialocephala in the topsoil and the ectomycorrhizal close-contact exploring Russula in cryoOM, whereas Sites 1 and 2 had a significantly higher mean proportion of plant pathogens and lichenized trophic modes. Co-occurrence network analysis revealed the lowest modularity and average path length, and highest clustering coefficient in cryoOM, which suggested a lower network resistance to environmental perturbation. Zi-Pi plot analysis suggested that some keystone taxa changed their role from generalist to specialist, depending on the specific horizon concerned, Cladophialophora in topsoil, saprotrophic Mortierella in cryoOM, and Penicillium in subsoil were classified as generalists for the respective horizons but specialists elsewhere. The litter saprotrophic taxon Cadophora finlandica played a role as a generalist in Site 1 and specialist in the rest of the sites. Overall, these results suggested that fungal communities within cryoOM were more susceptible to environmental change and some taxa may shift their role, which may lead to changes in carbon storage in permafrost-affected soil.

Pathogen Metagenomics Reveals Distinct Lung Microbiota Signatures Between Bacteriologically Confirmed and Negative Tuberculosis Patients

Understanding the dynamics of lung microbiota in tuberculosis patients, especially those who cannot be confirmed bacteriologically in clinical practice, is imperative for accurate diagnosis and effective treatment. This study aims to characterize the distinct lung microbial features between bacteriologically confirmed and negative tuberculosis patients to understand the influence of microbiota on tuberculosis patients. We collected specimens of bronchoalveolar lavage fluid from 123 tuberculosis patients. Samples were subjected to metagenomic next-generation sequencing to reveal the lung microbial signatures. By combining conventional bacterial detection and metagenomic sequencing, 101/123 (82%) tuberculosis patients were bacteriologically confirmed. In addition to Mycobacterium tuberculosis, Staphylococcus aureus, Kluyveromyces lactis, and Pyricularia pennisetigena were also enriched in the bacteriological confirmation group. In contrast, Haemophilus parainfluenzae was enriched in the bacteriologically negative group. Besides, microbial interaction exhibits a different state between bacteriologically confirmed and negative tuberculosis patients. Mycobacterium tuberculosis was confirmed correlated with clinical characteristics such as albumin and chest cavities. Our study comprehensively demonstrates the correlation between unique features of lung microbial dynamics and the clinical characteristics of tuberculosis patients, suggesting the importance of studying the pulmonary microbiome in tuberculosis disease and providing new insights for future precision diagnosis and treatment.

Engineering Multigenerational Host-Modulated Microbiota against Soilborne Pathogens in Response to Global Climate Change

Crop migration caused by climatic events has favored the emergence of new soilborne diseases, resulting in the colonization of new niches (emerging infectious diseases, EIDs). Soilborne pathogens are extremely persistent in the environment. This is in large part due to their ability to reside in the soil for a long time, even without a host plant, using survival several strategies. In this regard, disease-suppressive soils, characterized by a low disease incidence due to the presence of antagonist microorganisms, can be an excellent opportunity for the study mechanisms of soil-induced immunity, which can be applied in the development of a new generation of bioinoculants. Therefore, here we review the main effects of climate change on crops and pathogens, as well as the potential use of soil-suppressive microbiota as a natural source of biocontrol agents. Based on results of previous studies, we also propose a strategy for the optimization of microbiota assemblages, selected using a host-mediated approach. This process involves an increase in and prevalence of specific taxa during the transition from a conducive to a suppressive soil. This strategy could be used as a model to engineer microbiota assemblages for pathogen suppression, as well as for the reduction of abiotic stresses created due to global climate change.

Priority effects in microbiome assembly

Advances in next-generation sequencing have enabled the widespread measurement of microbiome composition across systems and over the course of microbiome assembly. Despite substantial progress in understanding the deterministic drivers of community composition, the role of historical contingency remains poorly understood. The establishment of new species in a community can depend on the order and/or timing of their arrival, a phenomenon known as a priority effect. Here, we review the mechanisms of priority effects and evidence for their importance in microbial communities inhabiting a range of environments, including the mammalian gut, the plant phyllosphere and rhizosphere, soil, freshwaters and oceans. We describe approaches for the direct testing and prediction of priority effects in complex microbial communities and illustrate these with re-analysis of publicly available plant and animal microbiome datasets. Finally, we discuss the shared principles that emerge across study systems, focusing on eco-evolutionary dynamics and the importance of scale. Overall, we argue that predicting when and how current community state impacts the success of newly arriving microbial taxa is crucial for the management of microbiomes to sustain ecological function and host health. We conclude by discussing outstanding conceptual and practical challenges that are faced when measuring priority effects in microbiomes.

Erosion reduces soil microbial diversity, network complexity and multifunctionality

While soil erosion drives land degradation, the impact of erosion on soil microbial communities and multiple soil functions remains unclear. This hinders our ability to assess the true impact of erosion on soil ecosystem services and our ability to restore eroded environments. Here we examined the effect of erosion on microbial communities at two sites with contrasting soil texture and climates. Eroded plots had lower microbial network complexity, fewer microbial taxa, and fewer associations among microbial taxa, relative to non-eroded plots. Soil erosion also shifted microbial community composition, with decreased relative abundances of dominant phyla such as Proteobacteria, Bacteroidetes, and Gemmatimonadetes. In contrast, erosion led to an increase in the relative abundances of some bacterial families involved in N cycling, such as Acetobacteraceae and Beijerinckiaceae. Changes in microbiota characteristics were strongly related with erosion-induced changes in soil multifunctionality. Together, these results demonstrate that soil erosion has a significant negative impact on soil microbial diversity and functionality.

Environmental vulnerability of the global ocean epipelagic plankton community interactome

Marine plankton form complex communities of interacting organisms at the base of the food web, which sustain oceanic biogeochemical cycles and help regulate climate. Although global surveys are starting to reveal ecological drivers underlying planktonic community structure and predicted climate change responses, it is unclear how community-scale species interactions will be affected by climate change. Here, we leveraged Tara Oceans sampling to infer a global ocean cross-domain plankton co-occurrence network-the community interactome-and used niche modeling to assess its vulnerabilities to environmental change. Globally, this revealed a plankton interactome self-organized latitudinally into marine biomes (Trades, Westerlies, Polar) and more connected poleward. Integrated niche modeling revealed biome-specific community interactome responses to environmental change and forecasted the most affected lineages for each community. These results provide baseline approaches to assess community structure and organismal interactions under climate scenarios while identifying plausible plankton bioindicators for ocean monitoring of climate change.

Manganese dioxide driven the carbon and nitrogen transformation by activating the complementary effects of core bacteria in composting

This study revealed core bacterial metabolic mechanisms involved in carbon (C) and nitrogen (N) in composting with adding MnO₂. Two tests (control group (CK), adding MnO₂ (M)) were performed. The results indicated that the MnO₂ accelerated the transformation of carbon and nitrogen in composting. Core bacteria involved in the C and N conversion were identified, the complementarity effects of core bacteria were stimulated in M composting. Additionally, the influence of core bacteria on the C and N conversion could be divided into two pathways in M composting. One was that core bacteria promoted C and N conversion by accelerating the flow of amino acids into the tricarboxylic acid cycle. Another was that the complementarity effects of core bacteria increased the overall bacterial diversity, which contributed to C and N conversion. These findings showed that the addition of MnO₂ to composting was a promising application to treat agricultural organic waste.

Enabling sustainable agriculture through understanding and enhancement of microbiomes

Harnessing plant-associated microbiomes offers an invaluable strategy to help agricultural production become more sustainable while also meeting growing demands for food, feed and fiber. A plethora of interconnected interactions among the host, environment and microbes, occurring both above and below ground, drive recognition, recruitment and colonization of plant-associated microbes, resulting in activation of downstream host responses and functionality. Dissecting these complex interactions by integrating multiomic approaches, high-throughput culturing, and computational and synthetic biology advances is providing deeper understanding of the structure and function of native microbial communities. Such insights are paving the way towards development of microbial products as well as microbiomes engineered with synthetic microbial communities capable of delivering agronomic solutions. While there is a growing market for microbial-based solutions to improve crop productivity, challenges with commercialization of these products remain. The continued translation of plant-associated microbiome knowledge into real-world scenarios will require concerted transdisciplinary research, cross-training of a next generation of scientists, and targeted educational efforts to prime growers and the general public for successful adoption of these innovative technologies.

Soil microbial interconnections along ecological restoration gradients of lowland forests after slash-and-burn agriculture

Microbial interconnections in soil are pivotal to ecosystem services and restoration. However, little is known about how soil microbial interconnections respond to slash-and-burn agriculture and to the subsequent ecosystem restoration after the practice. Here, we used amplicon sequencing and co-occurrence network analyses to explore the interconnections within soil bacterial and fungal communities in response to slash-and-burn practice and a spontaneous restoration (spanning ca. 60 years) of tropical forests after the practice, in Papua New Guinea. We found significantly higher complexity and greater variations in fungal networks than in those of bacteria, despite no significant changes observed in bacterial or fungal networks across successional stages. Within most successional stages, bacterial core co-occurrences (co-occurrences consistently present across all sub-networks in a stage) were more frequent than those of fungi, indicating higher stability of interconnections between bacteria along succession. The stable interconnections occurred frequently between bacterial taxa (i.e. Sporosarcina, Acidimicrobiale and Bacillaceae) and between ectomycorrhizal fungi (Boletaceae and Russula ochroleuca), implying important ecological roles of these taxa in the ecosystem restoration. Collectively, our results provide new insight into microbial interconnections in response to slash-and-burn agriculture and the subsequent ecosystem restoration, thus promoting a better understanding of microbial roles in ecosystem services and restoration.

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.

The soil crisis: the need to treat as a global health problem and the pivotal role of microbes in prophylaxis and therapy

Soil provides a multitude of services that are essential to a healthily functioning biosphere and continuity of the human race, such as feeding the growing human population and the sequestration of carbon needed to counteract global warming. Healthy soil availability is the limiting parameter in the provision of a number of these services. As a result of anthropogenic abuses, and natural and global warming-promoted extreme weather events, Planet Earth is currently experiencing an unprecedented crisis of soil deterioration, desertification and erosive loss that increasingly prejudices the services it provides. Such services are pivotal to the Sustainability Development Goals formulated by the United Nations. Immediate and coordinated action on a global scale is urgently required to slow and ultimately reverse the loss of healthy soils. Despite the 'dirt-dust', non-vital appearance of soil, it is a highly dynamic living entity, whose life is overwhelmingly microbial. The soil microbiota, which constitutes the greatest reservoir and donor of microbial diversity on Earth, acts as a vast bioreactor, mediating a myriad of chemical reactions that turn the biogeochemical cycles, recycle wastes, purify water, and underpin the multitude of other services soil provides. Fuelling the belowground microbial bioreactor is the aboveground plant and photosynthetic surface microbial life which captures solar energy, fixes inorganic CO2 to organic carbon, and channels fixed carbon and energy into soil. In order to muster an effective response to the crisis, to avoid further deterioration, and to restore unhealthy soils, we need a new and coherent approach, namely to deal with soils worldwide as patients in need of health care and create (i) a public health system for development of effective policies for land use, conservation, restoration, recommendations of prophylactic measures, monitoring and identification of problems (epidemiology), organizing crisis responses, etc., and (ii) a healthcare system charged with soil care: the promotion of good practices, implementation of prophylaxis measures, and institution of therapies for treatment of unhealthy soils and restoration of drylands. These systems need to be national but there is also a desperate need for international coordination. To enable development of effective, evidence-based strategies that will underpin the efforts of soil healthcare systems, a substantial investment in wide-ranging interdisciplinary research on soil health and disease is mandatory. This must lead to a level of understanding of the soil:biota functionalities underlying key ecosystem services that enables formulation of effective diagnosis-prophylaxis-therapy pathways for sustainable use, protection and restoration of different types of soil resources in different climatic zones. These conservation-regenerative-restorative measures need to be complemented by an educative-political-economic-legislative framework that provides incentives encouraging soil care: knowledge, policy, economic and others, and laws which promote international adherence to the principles of restorative soil management. And: we must all be engaged in improving soil health; everyone has a duty of care (https://www.bbc.co.uk/ideas/videos/why-soil-is-one-of-the-most-amazing-things-on-eart/p090cf64). Creative application of microbes, microbiomes and microbial biotechnology will be central to the successful operation of the healthcare systems.

Climate and Nutrient-Driven Regime Shifts of Cyanobacterial Communities in Low-Latitude Plateau Lakes

Cyanobacterial blooms that form in response to climate warming and nutrient enrichment in freshwater lakes have become a global environmental challenge. Historical legacy effects and the mechanisms underlying cyanobacterial community succession are not well understood, especially for plateau lakes that are important global freshwater resources. This study investigated the temporal dynamics of cyanobacterial communities over centuries in response to nutrient enrichment and climate warming in low-latitude plateau lakes using high-throughput DNA sequencing of sedimentary DNA combined with traditional paleolimnological analyses. Our results confirmed that nutrients and climate warming drive shifts in cyanobacterial communities over time. Cyanobacterial community turnover was pronounced with regime shifts toward new ecological states, occurring after exceeding a tipping point of aquatic total phosphorus (TP). The inferred species interactions, niche differentiation, and identity of keystone taxa significantly changed after crossing the aquatic TP ecological threshold, as demonstrated by network analysis of cyanobacterial taxa. Further, the contribution of aquatic TP to cyanobacterial community dynamics was greater than that of air temperature when lakes were in an oligotrophic state. In contrast, as the aquatic TP threshold was exceeded, the contribution to community dynamics by air temperature increased and potentially surpassed that of aquatic TP. Overall, these results provide new evidence for how past nutrient levels in lacustrine ecosystems influence contemporary cyanobacterial community responses to global warming in low-latitude plateau lakes.

The bacterial community structure and N-cycling gene abundance in response to dam construction in a riparian zone

Dam construction has significantly altered riparian hydrological regime and environmental conditions in the reservoir region, yet knowledge concerning how bacterial community and N-cycling genes respond to these changes remains limited. In this study, we investigated the bacterial community composition, network structure and N-cycling genes in the water level fluctuation zones (WLFZs) of the Three Gorges Reservoir (TGR). Here, samples collected from five different water levels were divided into three groups: waterward sediments, interface sediments, and landward soils. Our results show that higher contents of NO₂^--N, SOC, DOC, NH₄⁺-N, and TP were characterized in waterward and interface sediments whereas higherNO₃^--N content was observed in landward soils. The α-diversity of bacterial community decreased gradually from waterward sediments to landward soils. Compared with waterward sediments and landward soils, the interface sediments showed a unique bacterial community pattern with diverse primary producers as well as N-cycling microbes. The interface sediments also had a much more complex co-occurrence network and a higher possible community stability. Among all of N-cycling genes, higher abundances of nrfA and AOA amoA genes were observed in interface sediments. The dissimilarity in bacterial community composition and N-cycling gene abundance was mainly driven by water-level. Moreover, random forest model revealed that AOA amoA and nirS genes were the most sensitive indicators in response to water level fluctuations. Overall, this study suggests distinct abundance, diversity, and network structure of microbes in riparian sediments and soils across the gradient of water levels and enhances our understanding with respect to comprehensive effects of dam construction on nitrogen cycle.

Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring

Bioindication has become an indispensable part of water quality monitoring in most countries of the world, with the presence and abundance of bioindicator taxa, mostly multicellular eukaryotes, used for biotic indices. In contrast, microbes (bacteria, archaea and protists) are seldom used as bioindicators in routine assessments, although they have been recognized for their importance in environmental processes. Recently, the use of molecular methods has revealed unexpected diversity within known functional groups and novel metabolic pathways that are particularly important in energy and nutrient cycling. In various habitats, microbial communities respond to eutrophication, metals, and natural or anthropogenic organic pollutants through changes in diversity and function. In this review, we evaluated the common trends in these changes, documenting that they have value as bioindicators and can be used not only for monitoring but also for improving our understanding of the major processes in lotic and lentic environments. Current knowledge provides a solid foundation for exploiting microbial taxa, community structures and diversity, as well as functional genes, in novel monitoring programs. These microbial community measures can also be combined into biotic indices, improving the resolution of individual bioindicators. Here, we assess particular molecular approaches complemented by advanced bioinformatic analysis, as these are the most promising with respect to detailed bioindication value. We conclude that microbial community dynamics are a missing link important for our understanding of rapid changes in the structure and function of aquatic ecosystems, and should be addressed in the future environmental monitoring of freshwater ecosystems.

Environmental heterogeneity determines the ecological processes that govern bacterial metacommunity assembly in a floodplain river system

How diversity is structured has been a central goal of microbial ecology. In freshwater ecosystems, selection has been found to be the main driver shaping bacterial communities. However, its relative importance compared with other processes (dispersal, drift, diversification) may depend on spatial heterogeneity and the dispersal rates within a metacommunity. Still, a decrease in the role of selection is expected with increasing dispersal homogenization. Here, we investigate the main ecological processes modulating bacterial assembly in contrasting scenarios of environmental heterogeneity. We carried out a spatiotemporal survey in the floodplain system of the Paraná River. The bacterioplankton metacommunity was studied using both statistical inferences based on phylogenetic and taxa turnover as well as co-occurrence networks. We found that selection was the main process determining community assembly even at both extremes of environmental heterogeneity and homogeneity, challenging the general view that the strength of selection is weakened due to dispersal homogenization. The ecological processes acting on the community also determined the connectedness of bacterial networks associations. Heterogeneous selection promoted more interconnected networks increasing β-diversity. Finally, spatiotemporal heterogeneity was an important factor determining the number and identity of the most highly connected taxa in the system. Integrating all these empirical evidences, we propose a new conceptual model that elucidates how the environmental heterogeneity determines the action of the ecological processes shaping the bacterial metacommunity.

Anti-Tick Microbiota Vaccine Impacts Ixodes ricinus Performance during Feeding

The tick microbiota is a highly complex ensemble of interacting microorganisms. Keystone taxa, with a central role in the microbial networks, support the stability and fitness of the microbial communities. The keystoneness of taxa in the tick microbiota can be inferred from microbial co-occurrence networks. Microbes with high centrality indexes are highly connected with other taxa of the microbiota and are expected to provide important resources to the microbial community and/or the tick. We reasoned that disturbance of vector microbiota by removal of ubiquitous and abundant keystone bacteria may disrupt the tick-microbiota homeostasis causing harm to the tick host. These observations and reasoning prompted us to test the hypothesis that antibodies targeting keystone bacteria may harm the ticks during feeding on immunized hosts. To this aim, in silico analyses were conducted to identify keystone bacteria in the microbiota of Ixodes nymphs. The family Enterobacteriaceae was among the top keystone taxa identified in Ixodes microbiota. Immunization of α-1,3-galactosyltransferase-deficient-C57BL/6 (α1,3GT KO) mice with a live vaccine containing the Enterobacteriaceae bacterium Escherichia coli strain BL21 revealed that the production of anti-E. coli and anti-α-Gal IgM and IgG was associated with high mortality of I. ricinus nymphs during feeding. However, this effect was absent in two different strains of wild type mice, BALB/c and C57BL/6. This result concurred with a wide distribution of α-1,3-galactosyltransferase genes, and possibly α-Gal, in Enterobacteriaceae and other bacteria of tick microbiota. Interestingly, the weight of I. ricinus nymphs that fed on E. coli-immunized C57BL/6 was significantly higher than the weight of ticks that fed on C57BL/6 immunized with a mock vaccine. Our results suggest that anti-tick microbiota vaccines are a promising tool for the experimental manipulation of vector microbiota, and potentially the control of ticks and tick-borne pathogens.

Bacterial Operational Taxonomic Units Replace the Interactive Roles of Other Operational Taxonomic Units Under Strong Environmental Changes

Background

Microorganisms are an important component of an aquatic ecosystem and play a critical role in the biogeochemical cycle which influences the circulation of the materials and maintains the balance in aquatic ecosystems.

Objective

The seasonal variation along with the impact of anthropogenic activities, water quality, bacterial community composition and dynamics in the Loktak Lake, the largest freshwater lake of North East India, located in the Indo-Burma hotspot region was assessed during post-monsoon and winter season through metagenome analysis.

Methods

Five soil samples were collected during Post-monsoon and winter season from the Loktak Lake that had undergone different anthropogenic impacts. The metagenomic DNA of the soil samples was extracted using commercial metagenomic DNA extraction kits following the manufacturer’s instruction. The extracted DNA was used to prepare the NGS library and sequenced in the Illumina MiSeq platform.

Results

Metagenomics analysis reveals Proteobacteria as the predominant community followed by Acidobacteria and Actinobacteria. The presence of these groups of bacteria indicates nitrogen fixation, oxidation of iron, sulfur, methane, and source of novel antibiotic candidates. The bacterial members belonging to different groups were involved in various biogeochemical processes, including fixation of carbon and nitrogen, producing streptomycin, gramicidin and perform oxidation of sulfur, sulfide, ammonia, and methane.

Conclusion

The outcome of this study provides a valuable dataset representing a seasonal profile across various land use and analysis, targeting at establishing an understanding of how the microbial communities vary across the land use and the role of keystone taxa. The findings may contribute to searches for microbial bio-indicators as biodiversity markers for improving the aquatic ecosystem of the Loktak Lake.

Disentangling the seasonal co-occurrence patterns and ecological stochasticity of planktonic and benthic bacterial communities within multiple lakes

Both the planktonic bacterial community (PBC) and benthic bacterial community (BBC) are important for biogeochemical processes in freshwater lakes. Despite their ecological significance, little is known about their seasonal co-occurrence patterns and the ecological processes that drive them. In this study, we aimed to investigate the ecological associations among bacterial taxa and assembly processes of PBC and BBC in different seasons. We used 16S rRNA gene high-throughput sequencing of a total of 150 water and sediment samples collected from multiple lakes distributed in an urban region of China during winter and summer. Our results revealed that PBC showed stronger seasonal variations in co-occurrence patterns than BBC, suggesting that BBC had greater temporal stability than PBC. Winter PBC network was characterized by higher connectivity and complexity, and thereby the formation of a highly stable community structure; whereas lower connectivity arising from the presence of fewer predicted keystone taxa (hubs and connectors in a network) was destabilizing to summer PBC network. In addition, the phylum Firmicutes identified as a putative keystone taxon of PBC in both seasons played a non-negligible role in maintaining network structure which may result from strong functional associations with other bacterioplankton. Temperature and pH were the best explanatory factors predicting the seasonal co-occurrence patterns of PBC and BBC, respectively. Normalized stochasticity ratio based on null-model analysis indicated that deterministic processes overwhelmed stochastic processes in governing the assembly of PBC and BBC in both seasons. However, we observed a greater influence of ecological stochasticity on BBC assembly than PBC assembly in both seasons. Taken together, these findings provide insights into understanding the impacts of habitat heterogeneity and seasonal variability on microbial assemblage patterns in lake ecosystems.

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

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

Plant Grafting Shapes Complexity and Co-occurrence of Rhizobacterial Assemblages

Grafting is a basic technique which is widely used to increase yield and enhance biotic and abiotic stress tolerance in plant production. The diversity and interactions of rhizobacterial assemblages shaped by grafting are important for the growth of their hosts but remain poorly understood. To test the hypothesis that plant grafting shapes complexity and co-occurrence of rhizobacterial assemblage, four types of plants, including ungrafted bottle gourd (B), ungrafted watermelon (W), grafted watermelon with bottle gourd rootstock (W/B), and grafted bottle gourd with watermelon rootstock (B/W), were cultivated in two soil types in a greenhouse, and the rhizosphere bacterial communities were analyzed by 16S rRNA gene high-throughput sequencing. Both the soil type and grafting significantly influenced the bacterial community composition. Grafting increased bacterial within-sample diversity in both soils. Core enriched operational taxonomic units (OTUs) in the W/B rhizosphere compared with the other three treatments (B, W, and B/W) were mainly affiliated with Alphaproteobacteria, Deltaproteobacteria, and Bacteroidetes, which are likely related to methanol oxidation, methylotrophy, fermentation, and ureolysis. Co-occurrence network analysis proved that grafting increased network complexity, including the number of nodes, edges, and modules. Moreover, grafting strengthened the structural robustness of the network in the rhizosphere, while ungrafted watermelon had the lowest network robustness. Homogeneous selection played a predominant role in bacterial community assembly, and the contribution of dispersal limitation was increased in grafted watermelon with bottle gourd rootstock. Grafting increased the diversity and transformed the network topology of the bacterial community, which indicated that grafting could improve species coexistence in the watermelon rhizosphere.

Host and environmental determinants of microbial community structure in the marine phyllosphere

Although seagrasses are economically and ecologically critical species, little is known about their blade surface microbial communities and how these communities relate to the plant host. To determine microbial community composition and diversity on seagrass blade surfaces and in the surrounding seawater,16S rRNA gene sequencing (iTag) was used for samples collected at five sites along a gradient of freshwater input in the northern Gulf of Mexico on three separate sampling dates. Additionally, seagrass surveys were performed and environmental parameters were measured to characterize host characteristics and the abiotic conditions at each site. Results showed that Thalassia testudinum (turtle grass) blades hosted unique microbial communities that were distinct in composition and diversity from the water column. Environmental conditions, including water depth, salinity, and temperature, influenced community structure as blade surface microbial communities varied among sites and sampling dates in correlation with changes in environmental parameters. Microbial community composition also correlated with seagrass host characteristics, including growth rates and blade nutrient composition. There is some evidence for a core community for T. testudinum as 21 microorganisms from five phyla (Cyanobacteria, Proteobacteria, Planctomycetes, Chloroflexi, and Bacteroidetes) were present in all blade surface samples. This study provides new insights and understanding of the processes that influence the structure of marine phyllosphere communities, how these microbial communities relate to their host, and their role as a part of the seagrass holobiont, which is an important contribution given the current decline of seagrass coverage worldwide.

Biotic and abiotic factors shape arbuscular mycorrhizal fungal communities associated with the roots of the widespread fern Botrychium lunaria (Ophioglossaceae)

Arbuscular mycorrhizal fungi (AMF) play central roles in terrestrial ecosystems by interacting with both above and belowground communities as well as by influencing edaphic properties. The AMF communities associated with the roots of the fern Botrychium lunaria (Ophioglossaceae) were sampled in four transects at 2400 m a.s.l. in the Swiss Alps and analyzed using metabarcoding. Members of five Glomeromycota genera were identified across the 71 samples. Our analyses revealed the existence of a core microbiome composed of four abundant Glomus operational taxonomic units (OTUs), as well as a low OTU turnover between samples. The AMF communities were not spatially structured, which contrasts with most studies on AMF associated with angiosperms. pH, microbial connectivity and humus cover significantly shaped AMF beta diversity but only explained a minor fraction of variation in beta diversity. AMF OTUs associations were found to be significant by both cohesion and co-occurrence analyses, suggesting a role for fungus-fungus interactions in AMF community assembly. In particular, OTU co-occurrences were more frequent between different genera than among the same genus, rising the hypothesis of functional complementarity among the AMF associated to B. lunaria. Altogether, our results provide new insights into the ecology of fern symbionts in alpine grasslands.

Microbial community and interspecies interaction during grazing of ark shell bivalve (Scapharca subcrenata) in a full-scale bioremediation system of mariculture effluents

A novel biological approach using ark shell bivalves as potential species for remediation of effluents was studied to determine the microbial community interspecies interaction and nutrient cycling in a restoration system of mariculture effluents. A field study showed that Scapharca subcrenata was the main driver of the microbial community's interspecies-interaction (PERMANOVA, R = 0.0572, P = 0.005) in the treatment zone (TZ). Analysis of co-occurrence networks based on random matrix theory (RMT) indicated that the network's complexity parameters were enhanced in the TZ and disrupted in the control zone (CZ) due to eutrophic disturbances. Concurrently, the TZ was correlated with more profound network modifications (i.e., higher modularity, total nodes (n), cohesion, and proportion of positive links), suggesting that S. subcrenata influenced microbial interspecies interactions in the system. Similarly, the co-occurring networks of generalists Proteobacteria (OTU2037) at genus Anaerospora and Actinobacteria (OTU9660) at genus Candidatus aquiluna for anaerobic ammonia-oxidation (ANAMMOX) were highly significant in the TZ. The top-down and bottom-up forces of S. subcrenata influenced the removal efficiency of nitrogenous compounds by reducing 81.51% of nitrite (NO₂^--N), 84.61% of total ammonium nitrogen (TAN) and 72.78% of nitrate (NO₃^--N). Generally, the introduction of ark shell bivalve (S. subcrenata) to the system as a biofilter provides a very low-cost bioremediation technology that could be one of the best restorations and remediation tools for mariculture effluents.

Disruption of cross-feeding interactions by invading taxa can cause invasional meltdown in microbial communities

The strength of biotic interactions within an ecological community affects the susceptibility of the community to invasion by introduced taxa. In microbial communities, cross-feeding is a widespread type of biotic interaction that has the potential to affect community assembly and stability. Yet, there is little understanding of how the presence of cross-feeding within a community affects invasion risk. Here, I develop a metabolite-explicit model where native microbial taxa interact through both cross-feeding and competition for metabolites. I use this model to study how the strength of biotic interactions, especially cross-feeding, influence whether an introduced taxon can join the community. I found that stronger cross-feeding and competition led to much lower invasion risk, as both types of biotic interactions lead to greater metabolite scarcity for the invader. I also evaluated the impact of a successful invader on community composition and structure. The effect of invaders on the native community was greatest at intermediate levels of cross-feeding; at this ‘critical’ level of cross-feeding, successful invaders generally cause decreased diversity, decreased productivity, greater metabolite availability, and decreased quantities of metabolites exchanged among taxa. Furthermore, these changes resulting from a successful primary invader made communities further susceptible to future invaders. The increase in invasion risk was greatest when the network of metabolite exchange between taxa was minimally redundant. Thus, this model demonstrates a case of invasional meltdown that is mediated by initial invaders disrupting the metabolite exchange networks of the native community.

Aggregate size-dependence of bacterial community separation in a full-scale membrane bioreactor plant

The size of bacterial aggregates can determine both nutrient removal and sludge/water separation in activated sludge processes. In this study, the bacterial community structures and network associations of different sized aggregates obtained from a full-scale membrane bioreactor plant over a one-year period were investigated. Our results showed that biodiversity of larger sized aggregates was significantly higher than that of smaller ones and that the bacterial compositions of different sized aggregates differed significantly from each other. Bacteria related to nutrient removal (e.g. denitrification, hydrolysis and fermentation) were found to be significantly more abundant in larger aggregates than smaller ones. Network analysis revealed significant difference in species-species interactions, topological roles of individual OTU and keystone populations among different sized aggregates. Moreover, the occurrence of keystone OTUs affiliated with denitrifiers (Thermomonas) in networks of large and medium aggregates may suggest that denitrification influences bacterial interactions in large and medium aggregates. Overall, our results indicate the aggregates size-dependence of bacterial community separation in activated sludge. The current findings not only can provide guidance for process design and operation optimization, but also highlight the necessity for paying more attentions to the aggregate-based community, metabolic function and gene expression of activated sludge in future studies.

Interactions of PAH-degradation and nitrate-/sulfate-reducing assemblages in anaerobic sediment microbial community

Nitrate and sulfate are electron acceptors (EAs) for biodegradation of polycyclic aromatic hydrocarbons (PAHs) in anaerobic sediments. The efficiency of PAHs biodegradation depends on the strength of the interactions between PAH-degradation and EA-reduction assemblages. However, these interactions are less studied. In this study, microbial response and PAH degradation efficiencies in river sediment were investigated using nitrate and sulfate stimulation. Results showed that the functional assemblages (PAH-degraders, nitrate- and sulfate- reducers) were low connectivity in the microbial network without EA adding. Nitrate input rapidly (<1 day) raised the nitrate reduction intensity. And the PAH-degraders and nitrate reducers established significant and direct correlations under nitrate stimulation, seen from the 13 connectors (nodes) in the microbial network. In contrast, sulfate reducers slowly increased in abundance (>20 days) and were connected to PAH-degraders through indirect connection under sulfate stimulation. The null model suggested that nitrate led to a higher level of directional selection, which implied that nitrate was a more favorable EA to trigger the deterministic succession. As a result, PAHs degradation was faster with nitrate stimulation (t_1/2 = 68.3 d) than with sulfate stimulation (t_1/2 = 164.6 d). These mechanistic understandings can serve as the guidelines for EA selection in bioremediation.

Large-sized planktonic bioaggregates possess high biofilm formation potentials: Bacterial succession and assembly in the biofilm metacommunity

Wanted and unwanted surface-attached growth of bacteria is ubiquitous in natural and engineered settings. Normally, attachment of planktonic cells to media surfaces initiates biofilm formation and fundamentally regulates biofilm assembly processes. Here, culturing biofilm with planktonic sludge as source community, we found distinct succession profiles of biofilm communities sourced from the size-fractionated sludge flocs (<25; 25-120; >120 μm). Null model analyses revealed that deterministic process dominated in biofilm community assemblies but decreased with decreasing floc size. Additionally, the relative importance of environmental selection increased with increasing floc size of the source sludge, whereas homogenizing dispersal and ecological drift followed opposite trends. Phylogenetic molecular ecological networks (pMENs) indicated that species interactions were intensive in biofilm microbiota developed from large-sized flocs (>120 μm), as evidenced by the low modularity and harmonic geodesic distance and the high average degree. Intriguingly, the keystone taxa in these biofilm ecological networks were controlled by distinct interaction patterns but all showed strong habitat characteristics (e.g., facultative anaerobic, motile, hydrophobic and involved in extracellular polymeric substance metabolism), corroborating the crucial roles of environmental filtering in structuring biofilm community. Taken together, our findings highlight the role of planktonic floc properties in biofilm community assembly and advance our understanding of microbial ecology in biofilm-based systems.

Analysis of leaf microbiome composition of near-isogenic maize lines differing in broad-spectrum disease resistance

Plant genotype strongly affects disease resistance, and also influences the composition of the leaf microbiome. However, these processes have not been studied and linked in the microevolutionary context of breeding for improved disease resistance. We hypothesised that broad-spectrum disease resistance alleles also affect colonisation by nonpathogenic symbionts. Quantitative trait loci (QTL) conferring resistance to multiple fungal pathogens were introgressed into a disease-susceptible maize inbred line. Bacterial and fungal leaf microbiomes of the resulting near-isogenic lines were compared with the microbiome of the disease-susceptible parent line at two time points in multiple fields. Introgression of QTL from disease-resistant lines strongly shifted the relative abundance of diverse fungal and bacterial taxa in both 3-wk-old and 7-wk-old plants. Nevertheless, the effects on overall community structure and diversity were minor and varied among fields and years. Contrary to our expectations, host genotype effects were not any stronger in fields with high disease pressure than in uninfected fields, and microbiome succession over time was similar in heavily infected and uninfected plants. These results show that introgressed QTL can greatly improve broad-spectrum disease resistance while having only limited and inconsistent pleiotropic effects on the leaf microbiome in maize.

Impact of Cover Crops on the Soil Microbiome of Tree Crops

Increased concerns associated with interactions between herbicides, inorganic fertilizers, soil nutrient availability, and plant phytotoxicity in perennial tree crop production systems have renewed interest in the use of cover crops in the inter-row middles or between trees as an alternative sustainable management strategy for these systems. Although interactions between the soil microbiome and cover crops have been examined for annual cropping systems, there are critical differences in management and growth in perennial cropping systems that can influence the soil microbiome and, therefore, the response to cover crops. Here, we discuss the importance of cover crops in tree cropping systems using multispecies cover crop mixtures and minimum tillage and no-tillage to not only enhance the soil microbiome but also carbon, nitrogen, and phosphorus cycling compared to monocropping, conventional tillage, and inorganic fertilization. We also identify potentially important taxa and research gaps that need to be addressed to facilitate assessments of the relationships between cover crops, soil microbes, and the health of tree crops. Additional evaluations of the interactions between the soil microbiome, cover crops, nutrient cycling, and tree performance will allow for more effective and sustainable management of perennial cropping systems.

Bacterial networks mediate pentachlorophenol dechlorination across land-use types with citrate addition

Soil microorganisms play a crucial role in the bioremediation of pentachlorophenol (PCP)-contaminated soils. However, whether and how soil bacterial networks with keystone taxa affect PCP dechlorination is not well understood. The present study investigated the effects of citrate on soil bacterial networks mediating PCP dechlorination by direct and indirect transformation in iron-rich upland and paddy soils. The rates of PCP dechlorination and Fe(II) generation were accelerated by citrate addition, particularly in the paddy soils. Network analysis revealed that the topological properties of bacterial networks were changed by citrate addition; more modules and keystone taxa were significantly correlated with PCP dechlorination and Fe(II) generation in the networks. Random forest modeling indicated that Clostridiales was the most important bacterial order; it was significantly involved in both the direct and indirect pathways of PCP dechlorination. Citrate addition had less influence on the balance between the direct and indirect pathways of PCP dechlorination in the upland soils, whereas it enhanced biological PCP dechlorination more directly and efficiently in the paddy soils. Our results suggested that land-use type and citrate addition play a critical role in controlling the biogeochemical mechanisms of PCP dechlorination.

Analysis of interdomain taxonomic patterns in urban street mats

Streets are constantly crossed by billions of vehicles and pedestrians. Their gutters, which convey stormwater and contribute to waste management, and are important for human health and well-being, probably play a number of ecological roles. Street surfaces may also represent an important part of city surface areas. To better characterize the ecology of this yet poorly explored compartment, we used filtration and DNA metabarcoding to address microbial community composition and assembly across the city of Paris, France. Diverse bacterial and eukaryotic taxonomic groups were identified, including members involved in key biogeochemical processes, along with a number of parasites and putative pathogens of human, animals and plants. We showed that the beta diversity patterns between bacterial and eukaryotic communities were correlated, suggesting interdomain associations. Beta diversity analyses revealed the significance of biotic factors (cohesion metrics) in shaping gutter microbial community assembly and, to a lesser extent, the contribution of abiotic factors (pH and conductivity). Co-occurrences analysis confirmed contrasting non-random patterns both within and between domains of life, specifically when comparing diatoms and fungi. Our results highlight microbial coexistence patterns in streets and reinforce the need to further explore biodiversity in urban ground transportation infrastructures.

Fire affects the taxonomic and functional composition of soil microbial communities, with cascading effects on grassland ecosystem functioning

Fire is a crucial event regulating the structure and functioning of many ecosystems. Yet few studies have focused on how fire affects taxonomic and functional diversities of soil microbial communities, along with changes in plant communities and soil carbon (C) and nitrogen (N) dynamics. Here, we analyze these effects in a grassland ecosystem 9 months after an experimental fire at the Jasper Ridge Global Change Experiment site in California, USA. Fire altered soil microbial communities considerably, with community assembly process analysis showing that environmental selection pressure was higher in burned sites. However, a small subset of highly connected taxa was able to withstand the disturbance. In addition, fire decreased the relative abundances of most functional genes associated with C degradation and N cycling, implicating a slowdown of microbial processes linked to soil C and N dynamics. In contrast, fire stimulated above- and belowground plant growth, likely enhancing plant-microbe competition for soil inorganic N, which was reduced by a factor of about 2. To synthesize those findings, we performed structural equation modeling, which showed that plants but not microbial communities were responsible for significantly higher soil respiration rates in burned sites. Together, our results demonstrate that fire 'reboots' the grassland ecosystem by differentially regulating plant and soil microbial communities, leading to significant changes in soil C and N dynamics.

Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition

Microbial communities are increasingly recognized as crucial for animal health. However, our understanding of how microbial communities are structured across wildlife populations is poor. Mechanisms such as interspecific associations are important in structuring free-living communities, but we still lack an understanding of how important interspecific associations are in structuring gut microbial communities in comparison with other factors such as host characteristics or spatial proximity of hosts. Here, we ask how gut microbial communities are structured in a population of North American moose Alces alces. We identify key microbial interspecific associations within the moose gut and quantify how important they are relative to key host characteristics, such as body condition, for predicting microbial community composition. We sampled gut microbial communities from 55 moose in a population experiencing decline due to a myriad of factors, including pathogens and malnutrition. We examined microbial community dynamics in this population utilizing novel graphical network models that can explicitly incorporate spatial information. We found that interspecific associations were the most important mechanism structuring gut microbial communities in moose and detected both positive and negative associations. Models only accounting for associations between microbes had higher predictive value compared to models including moose sex, evidence of previous pathogen exposure or body condition. Adding spatial information on moose location further strengthened our model and allowed us to predict microbe occurrences with ~90% accuracy. Collectively, our results suggest that microbial interspecific associations coupled with host spatial proximity are vital in shaping gut microbial communities in a large herbivore. In this case, previous pathogen exposure and moose body condition were not as important in predicting gut microbial community composition. The approach applied here can be used to quantify interspecific associations and gain a more nuanced understanding of the spatial and host factors shaping microbial communities in non-model hosts.

Drivers and ecological consequences of dominance in periurban phytoplankton communities using networks approaches

Evaluating the causes and consequences of dominance by a limited number of taxa in phytoplankton communities is of huge importance in the current context of increasing anthropogenic pressures on natural ecosystems. This is of particular concern in densely populated urban areas where usages and impacts of human populations on water ecosystems are strongly interconnected. Microbial biodiversity is commonly used as a bioindicator of environmental quality and ecosystem functioning, but there are few studies at the regional scale that integrate the drivers of dominance in phytoplankton communities and their consequences on the structure and functioning of these communities. Here, we studied the causes and consequences of phytoplankton dominance in 50 environmentally contrasted waterbodies, sampled over four summer campaigns in the highly-populated Île-de-France region (IDF). Phytoplankton dominance was observed in 32-52% of the communities and most cases were attributed to Chlorophyta (35.5-40.6% of cases) and Cyanobacteria (30.3-36.5%). The best predictors of dominance were identified using multinomial logistic regression and included waterbody features (surface, depth and connection to the hydrological network) and water column characteristics (total N, TN:TP ratio, water temperature and stratification). The consequences of dominance were dependent on the identity of the dominant organisms and included modifications of biological attributes (richness, cohesion) and functioning (biomass, RUE) of phytoplankton communities. We constructed co-occurrence networks using high resolution phytoplankton biomass and demonstrated that networks under dominance by Chlorophyta and Cyanobacteria exhibited significantly different structure compared with networks without dominance. Furthermore, dominance by Cyanobacteria was associated with more profound network modifications (e.g. cohesion, size, density, efficiency and proportion of negative links), suggesting a stronger disruption of the structure and functioning of phytoplankton communities in the conditions in which this group dominates. Finally, we provide a synthesis on the relationships between environmental drivers, dominance status, community attributes and network structure.