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Aerobic granular sludge (AGS), a self-immobilized microbial consortium containing different functional microorganisms, is receiving growing attention, since it has shown great technological and economical potentials in the field of wastewater treatment. Microbial community is crucial for the formation, stability, and pollutant removal efficiency of aerobic granules. This mini-review systematically summarizes the recent findings of the microbial community structure and function of AGS and discusses the new research progress in the microbial community dynamics during the granulation process and spatial distribution patterns of the microbiota in AGS. The presented information may be helpful for the in-depth theoretical study and practical application of AGS technology in the future.

Ecological boundaries between different environments are important for generating and maintaining biodiversity and for understanding community assembly. Classic examples include temperature gradients between upland and lowland habitats and estuaries (brackish) between fresh- and saltwater. While numerous studies have examined community assembly of free-living organisms across ecological boundaries, few studies have considered community assembly of host-associated (HA) organisms, including HA microbiota, across similar ecological boundaries. This is likely because it is unclear what constitutes an ecological boundary for organisms that reside on a host. We identify hybrid hosts (i.e., hosts derived from breeding events between two different genetic lineages) as ecological boundaries for HA organisms. More specifically, we argue that the intermediate genetic compositions of hybrid organisms, often accompanied by traits that are either intermediate to or else combinations of progenitor traits, create transition zones between the environments experienced by microbes on or in progenitor host lineages. This, in turn, paves the way for microbial community coalescence (i.e., mixing of microbial communities) that is directly analogous to community assembly in classic ecological boundaries. Further, because many hybrid hosts reside along ecological boundaries themselves, hybrid microbiota often experience simultaneous boundaries of both their hosts and their hosts' environment-an underexplored phenomenon that we term a \"multiscale ecological boundary.\" By introducing ecological boundaries into HA microbiota literature, our goals are to further understanding of HA microbiota assembly and to propose a framework for studying the effects of ecological boundaries at multiple scales.IMPORTANCEBoundaries between environments provide important insight into how ecological communities are structured across broader landscapes. Of particular interest is how communities assemble within the transition zone constituting the boundary (i.e., where the transition in environmental variables occurs) and whether transitions in community composition parallel transitions in environmental variables. While ecological boundaries have a long history in classic ecology, similar concepts have recently emerged in microbiota literature. Currently, however, most studies of microbial ecological boundaries focus on environmental microbiota, rather than host-associated (HA) microbiota. This is likely because it is unclear what constitutes an ecological boundary in HA microbiota systems. We propose hybrid hosts as an HA analog for environmental ecological boundaries. Specifically, we outline how different types of hybrid hosts serve as models for different types of ecological boundaries. We then outline how the ecological boundary framework can be used to interpret HA microbial community coalescence (i.e., mixing) across host species. Finally, we suggest that many hybrid hosts reside within the transition zones of larger scale ecological boundaries. When this happens, hybrid hosts can be used to examine a novel phenomenon that we term a \"multiscale ecological boundary.\"

Diversity begets higher-order properties such as functional stability and robustness in microbial communities, but principles that inform conceptual (and eventually predictive) models of community dynamics are lacking. Recent work has shown that selection as well as dispersal and drift shape communities, but the mechanistic bases for assembly of communities and the forces that maintain their function in the face of environmental perturbation are not well understood. Conceptually, some interactions among community members could generate endogenous dynamics in composition, even in the absence of environmental changes. These endogenous dynamics are further perturbed by exogenous forcing factors to produce a richer network of community interactions and it is this ‘system’ that is the basis for higher-order community properties. Elucidation of principles that follow from this conceptual model requires identifying the mechanisms that (a) optimize diversity within a community and (b) impart community stability. The network of interactions between organisms can be an important element by providing a buffer against disturbance beyond the effect of functional redundancy, as alternative pathways with different combinations of microbes can be recruited to fulfill specific functions.

Microbial consortia have been used in biotechnology processes, including fermentation, waste treatment, and agriculture, for millennia. Today, synthetic biologists are increasingly engineering microbial consortia for diverse applications, including the bioproduction of medicines, biofuels, and biomaterials from inexpensive carbon sources. An improved understanding of natural microbial ecosystems, and the development of new tools to construct synthetic consortia and program their behaviors, will vastly expand the functions that can be performed by communities of interacting microorganisms. Here, we review recent advancements in synthetic biology tools and approaches to engineer synthetic microbial consortia, discuss ongoing and emerging efforts to apply consortia for various biotechnological applications, and suggest future applications. Microbial consortia exhibit advantages over monocultures, including division of labor, spatial organization, and robustness to perturbations. Synthetic biology tools are used to construct and control consortia by manipulating communication networks, regulating gene expression via exogenous inputs, and engineering syntrophic interactions. Synthetic biology approaches to control the behaviors of individual species within a consortium include population control, distribution of tasks, and spatial organization. Constructing microbial consortia is enhanced by computational models, which can predict preferred metabolic cross-feeding networks and infer population dynamics over time. Microbial biotechnology benefits from consortia due to the unique catalytic activities of each member, their ability to use complex substrates, compartmentalization of pathways, and distribution of molecular burden.

Aim: The aim was to explore how conversions of primary or secondary forests to plantations or agricultural systems influence soil microbial communities and soil carbon (C) cycling. Location: Global. Time period: 1993–2017. Major taxa studied: Soil microbes. Methods: A meta-analysis was conducted to examine effects of forest degradation on soil properties and microbial attributes related to microbial biomass, activity, community composition and diversity based on 408 cases from 119 studies in the world. Results: Forest degradation decreased the ratios of K-strategists to r-strategists (i.e., ratios of fungi to bacteria, Acidobacteria to Proteobacteria, Actinobacteria to Bacteroidetes and Acidobacteria + Actinobacteria to Proteobacteria + Bacteroidetes). The response ratios (RRs) of the K-strategist to r-strategist ratios to forest degradation decreased and increased with increased RRs of soil pH and soil C to nitrogen ratio (C:N), respectively. Forest degradation increased the bacterial alpha-diversity indexes, of which the RRs increased and decreased as the RRs of soil pH and soil C:N increased, respectively. The overall RRs across all the forest degradation types ranked as microbial C (−40.4%) > soil C (−33.3%) > microbial respiration (−18.9%) > microbial C to soil C ratio (qMBC; −15.9%), leading to the RRs of microbial respiration rate per unit microbial C (qCO2) and soil C decomposition rate (respiration rate per unit soil C), on average, increasing by +43.2 and +25.0%, respectively. Variances of the RRs of qMBC and qCO2 were significantly explained by the soil C, soil C:N and mean annual precipitation. Main conclusions: Forest degradation consistently shifted soil microbial community compositions from K-strategist dominated to r-strategist dominated, altered soil properties and stimulated microbial activity and soil C decomposition. These results are important for modelling the soil C cycling under projected global land-use changes and provide supportive evidence for applying the macroecology theory on ecosystem succession and disturbance in soil microbial ecology.

Microbial ecosystems are almost always dominated by only a few species, but their diversity resides in the rare biosphere. These rare members are usually considered passive passengers with little influence, yet our work reveals that they can collectively determine which species to become the most abundant taxon. We describe this process as a “nomination–voting” system: competitive traits nominate potential dominants, while rare taxa vote for the ultimate winner through their complex interactions. Recognizing this hidden but decisive role of rare microbes provides a new perspective on community assembly and underscores how subtle ecological interactions shape community outcomes. This assembly framework offers new opportunities for the prediction, manipulation, and stabilization of agriculture, health, and environmental microbiomes.

Plants depend upon beneficial interactions between roots and microbes for nutrient availability, growth promotion, and disease suppression. High-throughput sequencing approaches have provided recent insights into root microbiomes, but our current understanding is still limited relative to animal microbiomes. Here we present a detailed characterization of the root-associated microbiomes of the crop plant rice by deep sequencing, using plants grown under controlled conditions as well as field cultivation at multiple sites. The spatial resolution of the study distinguished three root-associated compartments, the endosphere (root interior), rhizoplane (root surface), and rhizosphere (soil close to the root surface), each of which was found to harbor a distinct microbiome. Under controlled greenhouse conditions, microbiome composition varied with soil source and genotype. In field conditions, geographical location and cultivation practice, namely organic vs. conventional, were factors contributing to microbiome variation. Rice cultivation is a major source of global methane emissions, and methanogenic archaea could be detected in all spatial compartments of field-grown rice. The depth and scale of this study were used to build coabundance networks that revealed potential microbial consortia, some of which were involved in methane cycling. Dynamic changes observed during microbiome acquisition, as well as steady-state compositions of spatial compartments, support a multistep model for root microbiome assembly from soil wherein the rhizoplane plays a selective gating role. Similarities in the distribution of phyla in the root microbiomes of rice and other plants suggest that conclusions derived from this study might be generally applicable to land plants.

Aim: Growing attention has been focused on the changes in the structure and diversity of microbial communities under altered precipitation pattern, but little is known about how this factor impacts microbial interactions. Our aim was to elucidate the variations of microbial interactions in semi-arid grassland soils and determine the key factor in regulating microbial assemblies in water–limited areas. Location: A c. 3,700 km transect across three habitats (desert, desert grassland and typical grassland) in Northern China. Time period: July and August 2012. Major taxa studied: Total bacteria and archaea. Method: The random matrix theory (RMT)-based network inference approach was used to construct species interaction networks. The relationships between microbial network topology and environmental variables were examined by Mantel and partial Mantel tests. Results: At the regional scale (across habitats), mean annual precipitation was the most important factor constraining the network structure, whereas at the local scale (within a habitat), soil conditions and plant parameters became more important, but their relative effects differed among habitats. In particular, no correlation was detected between the desert network and any environmental factors. The number of central species increased substantially in desert grassland and typical grassland networks in comparison to those in the desert network. Inter- and intra-module connections, particularly negative connections, also increased in the two grassland habitats. Main conclusions: Microbial networks become more complex as precipitation increases. A simple network structure (no connectors between modules, more sparsely distributed species and lower competitive links) and less association with environmental factors in the desert network indicate that microbial communities in extremely dry ecosystems are unstable and vulnerable; that is future climate change will greatly influence microbial interactions in these extremely dry areas. Overall, our findings provide new insight into the way in which microbes respond to changing precipitation patterns by regulating their interactions in water-limited ecosystems.

Terrestrial ecosystems worldwide are receiving increasing amounts of biologically reactive nitrogen (N) as a consequence of anthropogenic activities. This intended or unintended fertilization can have a wide‐range of impacts on biotic communities and hence on soil respiration. Reduction in below‐ground carbon (C) allocation induced by high N availability has been assumed to be a major mechanism determining the effects of N enrichment on soil respiration. In addition to increasing available N, however, N enrichment causes soil acidification, which may also affect root and microbial activities. The relative importance of increased N availability vs. soil acidification on soil respiration in natural ecosystems experiencing N enrichment is unclear. We conducted a 12‐year N enrichment experiment and a 4‐year complementary acid addition experiment in a semi‐arid Inner Mongolian grassland. We found that N enrichment had contrasting effects on root and microbial respiration. N enrichment significantly increased root biomass, root N content and specific root respiration, thereby promoting root respiration. In contrast, N enrichment significantly suppressed microbial respiration likely by reducing total microbial biomass and changing the microbial community composition. The effect on root activities was due to both soil acidity and increased available N, while the effect on microbes primarily stemmed from soil acidity, which was further confirmed by results from the acid addition experiment. Our results indicate that soil acidification exerts a greater control than soil N availability on soil respiration in grasslands experiencing long‐term N enrichment. These findings suggest that N‐induced soil acidification should be included in predicting terrestrial ecosystem C balance under future N deposition scenarios.

Phosphorus is an essential nutrient for all life on earth and has a major impact on plant growth and crop yield. The forms of phosphorus that can be directly absorbed and utilized by plants are mainly HPO42− and H2PO4−, which are known as usable phosphorus. At present, the total phosphorus content of soils worldwide is 400–1000 mg/kg, of which only 1.00–2.50% is plant-available, which seriously affects the growth of plants and the development of agriculture, resulting in a high level of total phosphorus in soils and a scarcity of available phosphorus. Traditional methods of applying phosphorus fertilizer cannot address phosphorus deficiency problems; they harm the environment and the ore material is a nonrenewable natural resource. Therefore, it is imperative to find alternative environmentally compatible and economically viable strategies to address phosphorus scarcity. Phosphorus-solubilizing bacteria (PSB) can convert insoluble phosphorus in the soil into usable phosphorus that can be directly absorbed by plants, thus improving the uptake and utilization of phosphorus by plants. However, there is no clear and systematic report on the mechanism of action of PSB. Therefore, this paper summarizes the discovery process, species, and distribution of PSB, focusing on the physiological mechanisms outlining the processes of acidolysis, enzymolysis, chelation and complexation reactions of PSB. The related genes regulating PSB acidolysis and enzymatic action as well as genes related to phosphate transport and the molecular direction mechanism of its pathway are examined. The effects of PSB on the structure and abundance of microbial communities in soil are also described, illustrating the mechanism of how PSB interact with microorganisms in soil and indirectly increase the amount of available phosphorus in soil. And three perspectives are considered in further exploring the PSB mechanism in utilizing a synergistic multi-omics approach, exploring PSB-related regulatory genes in different phosphorus levels and investigating the application of PSB as a microbial fungicide. This paper aims to provide theoretical support for improving the utilization of soil insoluble phosphorus and providing optimal management of elemental phosphorus in the future.