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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.

Minimal systematic research on the ecological interpretation of stone biodeterioration. This study reports dispersal limitation and heterogeneous selection shape the microbial community assembly responsible for the biodeterioration of red sandstone. Furthermore, fundamental metabolic processes of microbial communities, such as ammonium assimilation and nitrogen mineralization, are identified as contributors to stone biodeterioration. This study improves our understanding of microbial community assembly and their functional roles, providing a microbial ecological basis for developing effective strategies for the conservation of stone cultural heritage.

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.

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.

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.

Background Rhizodeposition is the release of organic compounds from plant roots into soil. Positive relationships between rhizodeposition and soil microbial biomass are commonly observed. Rhizodeposition may be disrupted by increasing drought however the effects of water stress on this process are not sufficiently understood. Scope We aimed to provide a synthesis of the current knowledge of drought impacts on rhizodeposition. The current scarcity of well-defined studies hinders a quantitative meta-analysis, but we are able to identify the main effects of water stress on this process and how changes in the severity of drought may produce different responses. We then give an overview of the links between rhizodeposition and microbial communities, and describe how drought may disrupt these interactions. Conclusions Overall, moderate drought appears to increase rhizodeposition per gram of plant, but under extreme drought rhizodeposition is more variable. Concurrent decreases in plant biomass may lessen the total amount of rhizodeposits entering the soil. Effects on rhizodeposition may be strongly species-dependant therefore impacts on soil communities may also vary, either driving subsequent changes or conferring resilience in the plant community. Advances in the study of rhizodeposition are needed to allow a deeper understanding of this plant-soil interaction and how it will respond to drought.

Coastal areas are land–sea transitional zones with complex natural and anthropogenic disturbances. Microorganisms in coastal sediments adapt to such disturbances both individually and as a community. The microbial community structure changes spatially and temporally under environmental stress. In this study, we investigated the microbial community structure in the sediments of Hangzhou Bay, a seriously polluted bay in China. In order to identify the roles and contribution of all microbial taxa, we set thresholds as 0.1% for rare taxa and 1% for abundant taxa, and classified all operational taxonomic units into six exclusive categories based on their abundance. The results showed that the key taxa in differentiating the communities are abundant taxa (AT), conditionally abundant taxa (CAT), and conditionally rare or abundant taxa (CRAT). A large population in conditionally rare taxa (CRT) made this category collectively significant in differentiating the communities. Both bacteria and archaea demonstrated a distance decay pattern of community similarity in the bay, and this pattern was strengthened by rare taxa, CRT and CRAT, but weakened by AT and CAT. This implied that the low abundance taxa were more deterministically distributed, while the high abundance taxa were more ubiquitously distributed. Based on a full-scale microbial taxa classification, the roles and contributions of key taxonomic categories in maintaining and altering microbial community structures in the sediments of Hangzhou Bay were recognized.

Granular activated sludge has gained increasing interest due to its potential in treating wastewater in a compact and efficient way. It is well-established that activated sludge can form granules under certain environmental conditions such as batch-wise operation with feast-famine feeding, high hydrodynamic shear forces, and short settling time which select for dense microbial aggregates. Aerobic granules with stable structure and functionality have been obtained with a range of different wastewaters seeded with different sources of sludge at different operational conditions, but the microbial communities developed differed substantially. In spite of this, granule instability occurs. In this review, the available literature on the mechanisms involved in granulation and how it affects the effluent quality is assessed with special attention given to the microbial interactions involved. To be able to optimize the process further, more knowledge is needed regarding the influence of microbial communities and their metabolism on granule stability and functionality. Studies performed at conditions similar to full-scale such as fluctuation in organic loading rate, hydrodynamic conditions, temperature, incoming particles, and feed water microorganisms need further investigations.

Metabolic enzyme activity and microbial composition of the air-curing and fermentation processes determine the quality of cigar tobacco leaves (CTLs). In this study, we reveal the evolution of the dominant microorganisms and microbial community structure at different stages of the air-curing and fermentation processes of CTLs. The results showed that the changes in metabolic enzymes occurred mainly during the air-curing phase, with polyphenol oxidase (PPO) being the most active at the browning phase. Pseudomonas, Bacteroides, Vibrio, Monographella, Bipolaris, and Aspergillus were the key microorganisms in the air-curing and fermentation processes. Principal coordinate analysis revealed significant separation of microbial communities between the air-curing and fermentation phases. Redundancy analysis showed that bacteria such as Proteobacteria, Firmicutes, Bacteroidota, and Acidobacteriota and fungi such as Ascomycota and Basidiomycota were correlated with enzyme activity and temperature and humidity. Bacteria mainly act in sugar metabolism, lipid metabolism, and amino acid metabolism, while fungi mainly degrade lignin, cellulose, and pectin through saprophytic action. Spearman correlation network analysis showed that Firmicutes, Proteobacteria, and Actinobacteria were the key bacterial taxa, while Dothideomycetes, Sordariomycetes, and Eurotiomycetes were the key fungal taxa. This research provides the basis for improving the quality of cigars by improving the air-curing and fermentation processes.Key points• Changes in POD and PPO activity control the color change of CTLs at the air-curing stage.• Monographella, Aspergillus, Pseudomonas, and Vibrio play an important role in air-curing and fermentation.• Environmental temperature and humidity mainly affect the fermentation process, whereas bacteria such as Proteobacteria, Firmicutes, Bacteroidota, and Acidobacteriota and fungi such as Ascomycota and Basidiomycota are associated with enzyme activity and temperature and humidity.