Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters

Enhancing methane production in two-phase anaerobic digestion of perishable organic waste: Mini-review on acidogenic fermentation pathways and regulatory strategies

Two-phase anaerobic digestion is a highly effective approach for efficient reduction and resource recovery of perishable organic waste. Within this technological framework, organic wastes undergo multiple metabolic pathways during the acidogenic phase, which is classified into ethanol, butyrate, propionate, lactate, and mixed acid fermentation depending on the acidification end products. The nature of these acidification products critically influences the performance of the subsequent methanogenic phase. Strategic regulation of operational parameters during the acidogenic phase fosters the enrichment of specific microbial communities and establishment of dominant consortia, which enable the production of the targeted acidification end-products. This review provides a comprehensive analysis of the metabolic characteristics and regulatory strategies associated with various acidogenic fermentation types and methanogenic properties of different acidification products. The findings presented here are crucial for enhancing the stability and methanogenic efficiency of anaerobic digestion systems that process perishable organic waste.

Graph-based deep learning for predictions on changes in microbiomes and biogas production in anaerobic digestion systems

Anaerobic digestion (AD), which relies on a complex microbial consortium for efficient biogas generation, is a promising avenue for renewable energy production and organic waste treatment. However, understanding and optimising AD processes are challenging because of the intricate interactions within microbial communities and the impact of volatile fatty acids (VFAs) on biogas production. To address these challenges, this study proposes the application of graph convolutional networks (GCNs) to comprehensively model AD processes. GCN models were developed to predict microbial dynamics and biogas production by integrating network analyses of high-throughput sequencing data and VFA inhibition effects. The models were trained based on the responses of anaerobic digesters to organic loading rate shock, starvation, and bioaugmentation for 281 d under various feeding conditions. Shifts in microbial community composition during AD stages and feeding conditions were successfully identified using next-generation sequencing tools. Graph topological features indicated a significant coupling between VFAs and microbial families, and the hydrogenotrophic archaeal families were most frequently connected to other families or residual acids. The GCN accurately predicted microbial abundances and gas production rates, achieving a mean squared error of 0.11 and 0.01 and a coefficient of determination of 0.72 and 0.87 for the testing dataset. These results provide valuable insights into the effects of starvation and bioaugmentation on the microbiome by utilising GCNs to model anaerobic treatment processes, predict microbial dynamics, and assess reactor productivity. Our study suggests a new modelling framework for understanding and improving AD systems by considering microbial interaction networks in relation to chemical parameter information at relevant operating scales.

Overcoming Extreme Ammonia Inhibition on Methanogenesis by Artificially Constructing a Synergistically Community with Acidogenic Bacteria and Hydrogenotrophic Archaea

High total ammonia nitrogen (TAN) inhibits anaerobic digestion (AD) and cannot be completely eliminated by merely enhancing a stage of AD. This study incorporates TAN-tolerant inoculum into substrates hydrolyzed by Rhizopus mixed agents to simultaneously enhance hydrolysis-acidogenesis-methanogenesis. The results show a 16.46-fold increase in CH4 production under TAN-inhibited (6870.97 mg L-1) conditions, even exceeding the AD without TAN by 21.10%. Model substrates sodium acetate and mixed H2 confirm hydrogenotrophic methanogenesis is the main pathway, with reduced TAN inhibition. Furthermore, a synergistic metabolic microbial community dominated by hydrolytic bacteria JAAYGG01 sp. and DTU014 sp., acidogenic bacteria DTU015 sp., DTU013 sp., and JAAYLO01 sp., and methanogens Methanosarcina mazei and an unclassified species in the Methanoculleus is reconstructed to resist TAN inhibition. Metagenomic combined with metatranscriptomic sequencing identifies that this microbial community carries xynD and bglB to regulate substrate hydrolysis, leading to acetate production through glycolysis, butyrate, and pyruvate metabolism with high acetate kinase activity, thereby CH4 produced primarily via hydrogenotrophic methanogenesis with high coenzyme F420 activity, facilitated by efficient mass transfer processes and quorum sensing regulation. This cleaner strategy obtains higher economic benefit (US$149.02) than conventional AD and can increase 154.64-fold energy production of a 24 000 m3 biogas plant, guided by machine learning.

Microbial functional guilds respond cohesively to rapidly fluctuating environments

Microbial communities experience environmental fluctuations across timescales from rapid changes in moisture, temperature, or light levels to long-term seasonal or climactic variations. Understanding how microbial populations respond to these changes is critical for predicting the impact of perturbations, interventions, and climate change on communities. Since communities typically harbor tens to hundreds of distinct taxa, the response of microbial abundances to perturbations is potentially complex. However, while taxonomic diversity is high, in many communities taxa can be grouped into functional guilds of strains with similar metabolic traits. These guilds effectively reduce the complexity of the system by providing a physiologically motivated coarse-graining. Here, using a combination of simulations, theory, and experiments, we show that the response of guilds to nutrient fluctuations depends on the timescale of those fluctuations. Rapid changes in nutrient levels drive cohesive, positively correlated abundance dynamics within guilds. For slower timescales of environmental variation, members within a guild begin to compete due to similar resource preferences, driving negative correlations in abundances between members of the same guild. Our results provide a route to understanding the relationship between functional guilds and community response to changing environments, as well as an experimental approach to discovering functional guilds via designed nutrient perturbations to communities.

Accelerated stochastic processes of plankton community assembly due to tidal restriction by seawall construction in the Yangtze River Estuary

Seawall construction has complex ecological impacts. However, the ecological mechanisms within plankton communities under tidal restriction resulting from seawall construction remain unexplored. Using environmental DNA (eDNA) metabarcoding, this study examined the impact of seawall construction on the assembly process of planktonic eukaryote and bacteria communities from the unrestricted area and the tide-restricted area in the Chongming Dongtan Nature Reserve of Yangtze River Estuary. While environmental heterogeneity did not exert a significant influence on alpha diversity of plankton, it had a significant impact on community structure. Variation partitioning analysis (VPA) and neutral community model indicated that neither environmental nor spatial factors were predominant drivers of plankton community composition and structure, instead, they were influenced by stochastic processes. Moreover, it was observed that the relative significance of stochastic processes in the tide-restricted area exceeded that in the unrestricted area. High habitat uniformity and water connectivity resulting from seawall construction may facilitate homogenization and spread among high-abundance groups. The results have significant implications for understanding the mechanisms underlying succession and composition, and for improving ecological assessment and remediation efforts in areas impacted by tidal restriction.

Structure and assembly mechanisms of the microbial community on an artificial reef surface, Fangchenggang, China

The construction of artificial reefs (ARs) is an effective way to restore habitats and increase and breed fishery resources in marine ranches. However, studies on the impacts of ARs on the structure, function, and assembly patterns of the bacterial community (BC), which is important in biogeochemical cycles, are lacking. The compositions, diversities, assembly patterns, predicted functions, and key environmental factors of the attached and free-living microbial communities in five-year ARs (O-ARs) and one-year ARs (N-ARs) in Fangchenggang, China, were analyzed via 16S rRNA gene sequencing. Proteobacteria was the dominant taxon in all the samples, with an average relative abundance of 44.48%, followed by Bacteroidetes (17.42%) and Cyanobacteria (15.19%). The composition of bacterial phyla was similar between O-ARs and N-ARs, but the relative abundance of Cyanobacteria was greater in the water column (38.56%) than on the AR surface (mean of 7.40%). The results revealed that the Shannon‒Wiener diversity indices were 5.64 and 5.45 for O-ARs and N-ARs, respectively. Principal coordinate analysis (PCoA) revealed different distributions of O-ARs and N-ARs in the microbial community. Additionally, network analysis revealed that the bacterial community was more complex and stable in O-ARs than in N-ARs, indicating that the 5-year AR presented a more diverse and stable microbial community overall. The KEGG database was used to predict that nitrogen metabolism, carbon metabolism, and membrane transport were the dominant microbial functions, accounting for 29.93% of the total functional abundances. The results of the neutral community model revealed that stochastic processes (67.2%) dominated the assembly of BCs. Interestingly, deterministic processes may be increasingly important in community aggregation over time. Moreover, a null model revealed that dispersal limitation was the most important process among the stochastic processes, accounting for 57.14% of the total. In addition, redundancy analysis (RDA) revealed that hydrological factors obviously impacted the structure and function of the microbial community. Our results showed that the construction of ARs slightly promotes local diversities in the structure and function of the microbial community, indicating it requires a longer time to enhance the diversity of the microbial community on artificial reefs. KEY POINTS: • Artificial reefs facilitate the diversity and functions of the microbial community • Stochastic processes dominate the assembly of the microbial community in artificial reefs • Nitrogen and carbon metabolism dominate microbial functions in artificial reefs.

Exogenous additives reshape the microbiome and promote the reduction of resistome in co-composting of pig manure and mushroom residue

Comprehensive understanding of the microbiome and resistome evolution in compost is crucial for guaranteeing the safety of organic fertilizers. Current studies using different composting systems and sequencing technologies have yielded varying conclusions on the efficacy of exogenous additives (EAs) in reducing antibiotic resistance genes (ARGs) in compost. This study employed metagenomics to investigate the impact of various EAs on microbial communities, ARGs, their coexistence with mobile genetic elements (MGEs), and ARG hosts in co-composting. Our results demonstrated that EAs significantly reshaped the microbial communities and facilitated a notable reduction in total ARG abundance and diversity, primarily by decreasing core ARGs. Cooperative rather than antagonistic relationships among bacteria. The RA changes in total ARGs are mainly caused by a decrease in the prevalence of core ARGs. Furthermore, EAs showed significant efficacy in reducing clinical ARGs, including cfxA, tetX1, cfxA6, vanA, and aac (6')-Ib', with diatomite (5 %) and zeolite (5 %) being the most effective. The effect of EAs on ARGs and microbial community assembly were stochastic processes. Composting stage and EAs jointly reduced the association between ARGs and MGEs in the composting system. The reduction of ARGs attributed to a decreased abundance of potential pathogenic ARG-associated hosts and diminished associations with MGEs. In conclusion, EAs present a straightforward and effective approach for promoting ARGs reduction in compost, offering crucial insights for assessing the environmental risks associated with the release of agricultural ARGs.

Temporal Changes in the Role of Species Sorting and Evolution Determine Community Dynamics

Evolutionary change within community members and shifts in species composition via species sorting contribute to community and trait dynamics. However, we do not understand when and how both processes contribute to community dynamics. Here, we estimated the contributions of species sorting and evolution over time (60 days) in bacterial communities of 24 species under selection by a ciliate predator. We found that species sorting contributed to increased community carrying capacity, while evolution contributed to decreased anti-predator defences. The relative roles of both processes changed over time, and our analysis indicates that if initial trait variation was in the direction of selection, species sorting prevailed, otherwise evolution drove phenotypic change. Furthermore, community composition, population densities and genomic evolution were affected by phenotypic match-mismatch combinations of predator and prey evolutionary history. Overall, our findings help to integrate when and how ecological and evolutionary processes structure communities.

Dispersal shapes compositional and functional diversity in aquatic microbial communities

Segregation and mixing shape the structure and functioning of aquatic microbial communities, but their respective roles are challenging to disentangle in field studies. We explored the hypothesis that functional differences and beta diversity among stochastically assembled communities would increase in the absence of dispersal. Contrariwise, we expected biotic selection during homogenizing dispersal to reduce beta and gamma diversity as well as functional variability. This was experimentally addressed by examining the compositional and functional changes of 20 freshwater bacterial assemblages maintained at identical conditions over seven growth cycles for 34 days and subjected to two consecutive dispersal regimes. Initial dispersal limitation generated high beta diversity and led to the repeated emergence of community types that were dominated by particular taxa. Compositional stability and evenness of the community types varied over successive growth cycles, reflecting differences in functional properties. Carbon use efficiency increased during cultivation, with some communities of unique composition outperforming the replicate community types. Homogenizing dispersal led to high compositional similarity and reduced gamma diversity. While a neutral and a competition-based (Elo-rating) model together largely explained community assembly, a pseudomonad disproportionally dominated across communities, possibly due to interaction-related genomic traits. In conclusion, microbial assemblages stochastically generated by dispersal limitation can be gradually "refined" into distinct community types by subsequent deterministic processes. Segregation of communities represented an insurance mechanism for highly productive but competitively weak microbial taxa that were excluded during community coalescence.

IMPORTANCE

We experimentally assessed the compositional and functional responses of freshwater bacterial assemblages exposed to two consecutive dispersal-related events (dispersal limitation and homogenizing dispersal) under identical growth conditions. While segregation led to a decreased local diversity, high beta diversity sustained regional diversity and functional variability. In contrast, homogenizing dispersal reduced the species pool and functional variability of the metacommunity. Our findings highlight the role of dispersal in regulating both diversity and functional variability of aquatic microbial metacommunities, thereby providing crucial insight to predict changes in ecosystem functioning.

Long-Read Sequencing Revealing the Effectiveness of Captive Breeding Strategy for Improving the Gut Microbiota of Spotted Seal (Phoca largha)

The spotted seal (Phoca largha) is the sole pinniped species that can reproduce in China and has been classified as the First-Grade State Protection animal. The conventional method for the protection and maintenance of the spotted seal population is the captive maintenance of the species in artificially controlled environments. Nevertheless, the efficacy of the captive strategy remains uncertain, with the potential to impact the health of spotted seals through alterations in gut microbiota. In this study, PacBio sequencing based on the full-length of the bacterial 16S rRNA gene was applied to faeces from captive and wild spotted seals, thereby providing a first reference for the gut microbiota profile of spotted seals at the species scale. The gut microbiota of captive spotted seals was found to be more diverse than that of the wild population. The gut microbiota of spotted seals exhibited notable variation due to captive breeding, with an enrichment of Firmicutes and a reduction in Proteobacteria. The results of the co-occurrence network analysis indicated that the gut microbiota of captive spotted seals exhibited a greater degree of complexity and stability in comparison to that observed in their wild counterparts. The analysis of community assembly mechanisms revealed an increased determinism for the gut microbiota of captive individuals, with a concomitant decrease in the contribution of drift. Furthermore, the results of the predicted functions indicated a reduction in stress responses and an enhanced ability to metabolise sugars in the gut microbiota of captive spotted seals. In conclusion, the results of this study provide evidence that the current captive breeding strategy is an effective approach for improving the gut microbiota of spotted seals. Furthermore, this study demonstrates the potential of monitoring the gut microbiota to assess the health of marine mammals and inform conservation strategies for endangered species.

Inoculum source determines the stress resistance of electroactive functional taxa in biofilms: A metagenomic perspective

The inoculum has a crucial impact on bioreactor initialization and performance. However, there is currently a lack of guidance on selecting appropriate inocula for applications in environmental biotechnology. In this study, we applied microbial electrolysis cells (MECs) as models to investigate the differences in the functional potential of electroactive microorganisms (EAMs) within anodic biofilms developed from four different inocula (natural or artificial), using shotgun metagenomic techniques. We specifically focused on extracellular electron transfer (EET) function and stress resistance, which affect the performance and stability of MECs. Community profiling revealed that the family Geobacteraceae was the key EAM taxon in all biofilms, with Geobacter as the dominant genus. The c-type cytochrome gene imcH showed universal importance for Geobacteraceae EET and was utilized as a marker gene to evaluate the EET potential of EAMs. Additionally, stress response functional genes were used to assess the stress resistance potential of Geobacter species. Comparative analysis of imcH gene abundance revealed that EAMs with comparable overall EET potential could be enriched from artificial and natural inocula (P > 0.05). However, quantification of stress response gene copy numbers in the genomes demonstrated that EAMs originating from natural inocula possessed superior stress resistance potential (196 vs. 163). Overall, this study provides novel perspectives on the inoculum effect in bioreactors and offers theoretical guidance for selecting inoculum in environmental engineering applications.

Unveiling the deterministic dynamics of microbial meta-metabolism: a multi-omics investigation of anaerobic biodegradation

BACKGROUND

Microbial anaerobic metabolism is a key driver of biogeochemical cycles, influencing ecosystem function and health of both natural and engineered environments. However, the temporal dynamics of the intricate interactions between microorganisms and the organic metabolites are still poorly understood. Leveraging metagenomic and metabolomic approaches, we unveiled the principles governing microbial metabolism during a 96-day anaerobic bioreactor experiment.

RESULTS

During the turnover and assembly of metabolites, homogeneous selection was predominant, peaking at 84.05% on day 12. Consistent dynamic coordination between microbes and metabolites was observed regarding their composition and assembly processes. Our findings suggested that microbes drove deterministic metabolite turnover, leading to consistent molecular conversions across parallel reactors. Moreover, due to the more favorable thermodynamics of N-containing organic biotransformations, microbes preferentially carried out sequential degradations from N-containing to S-containing compounds. Similarly, the metabolic strategy of C18 lipid-like molecules could switch from synthesis to degradation due to nutrient exhaustion and thermodynamical disadvantage. This indicated that community biotransformation thermodynamics emerged as a key regulator of both catabolic and synthetic metabolisms, shaping metabolic strategy shifts at the community level. Furthermore, the co-occurrence network of microbes-metabolites was structured around microbial metabolic functions centered on methanogenesis, with CH4 as a network hub, connecting with 62.15% of total nodes as 1st and 2nd neighbors. Microbes aggregate molecules with different molecular traits and are modularized depending on their metabolic abilities. They established increasingly positive relationships with high-molecular-weight molecules, facilitating resource acquisition and energy utilization. This metabolic complementarity and substance exchange further underscored the cooperative nature of microbial interactions.

CONCLUSIONS

All results revealed three key rules governing microbial anaerobic degradation. These rules indicate that microbes adapt to environmental conditions according to their community-level metabolic trade-offs and synergistic metabolic functions, further driving the deterministic dynamics of molecular composition. This research offers valuable insights for enhancing the prediction and regulation of microbial activities and carbon flow in anaerobic environments. Video Abstract.

Impacts of eutrophication on microbial community structure in sediment, seawater, and phyllosphere of seagrass ecosystems

Introduction

Seagrass-associated microbial communities play a crucial role in the growth and health of seagrasses. However, like seagrass meadows, seagrass-associated microbial communities are often affected by eutrophication. It remains unclear how eutrophication influences the composition and function of microbial communities associated with different parts of seagrass.

Methods

We employed prokaryotic 16S rRNA gene high-throughput sequencing combining microbial community structure analysis and co-occurrence network analysis to investigate variances in microbial community compositions, potential functions and complexities across sediment, seagrass leaves, and seawater within different eutrophic areas of two adjacent seagrass meadows on Hainan Island, China.

Results

Our results indicated that microbial diversity on seagrass leaves was significantly lower than in sediment but significantly higher than in seawater. Both sediment and phyllosphere microbial diversity showed no significant difference between the highly eutrophic and less eutrophic sites in each lagoon. However, sediment microbial diversity was higher in the more eutrophic lagoon, while phyllosphere microbial diversity was higher in the less eutrophic lagoon. Heavy eutrophication increased the relative abundance of phyllosphere microorganisms potentially involved in anaerobic metabolic processes, while reducing those responsible for beneficial functions like denitrification. The main factor affecting microbial diversity was organic carbon in seawater and sediment, with high organic carbon levels leading to decreased microbial diversity. The co-occurrence network analysis revealed that heavy eutrophication notably reduced the complexity and internal connections of the phyllosphere microbial community in comparison to the sediment and seawater microbial communities. Furthermore, ternary analysis demonstrated that heavy eutrophication diminished the external connections of the phyllosphere microbial community with the sediment and seawater microbial communities.

Conclusion

The pronounced decrease in biodiversity and complexity of the phyllosphere microbial community under eutrophic conditions can lead to greater microbial functional loss, exacerbating seagrass decline. This study emphasizes the significance of phyllosphere microbial communities compared to sediment microbial communities in the conservation and restoration of seagrass meadows under eutrophic conditions.

Seasonal variations affect the ecosystem functioning and microbial assembly processes in plantation forest soils

While afforestation mitigates climate concerns, the impact of afforestation on ecological assembly processes and multiple soil functions (multifunctionality) in afforested areas remains unclear. The Xiong'an New Area plantation forests (Pinus and Sophora forests) in North China were selected to examine the effects of plantation types across four distinct seasons on soil microbiomes. Three functional categories (nutrient stocks, organic matter decomposition, and microbial functional genes) of multifunctionality and the average (net) multifunctionality were quantified. All these categories are directly related to soil functions. The results showed that net soil multifunctionality as a broad function did not change seasonally, unlike other narrow functional categories. Bacterial communities were deterministically (variable selection and homogenous selection) structured, whereas the stochastic process of dispersal limitation was mainly responsible for the assembly and turnover of fungal and protist communities. In Pinus forests, winter initiates a sudden shift from deterministic to stochastic processes in bacterial community assembly, accompanied by decreased Shannon diversity and heightened nutrient cycling (nutrient stocks and organic matter decomposition). This indicates the potential vulnerability of deterministic assembly to seasonal fluctuations, particularly in environments rich in nutrients. The results predicted that protist community composition was uniquely structured with C-related functional activities relative to bacterial and fungal β-diversity variations, which were mostly explained by seasonal variations. Our study highlighted the importance of the protist phagocytosis process on soil microbial interactions through the predicted impact of protist α-diversity on microbial cooccurrence network parameters. This association might be driven by the high abundance of protist consumers as the main predators of bacterial and fungal lineages in our sampling plots. Our findings reveal that the complexity of microbial co-occurrence interactions was considerably higher in spring, perhaps attributing thermal variability and increased resource availability within spring that foster microbial diversity and network complexity. This study contributes to local ecosystem prospects to model the behavior of soil biota seasonally and their implied effects on soil functioning and microbial assembly processes, which will benefit global-scale afforestation programs by promoting novel, precise, and rational plantation forests for future environmental sustainability and self-sufficiency.

Epiphytic bacterial community composition on four submerged macrophytes in different regions of Taihu Lake

The epiphytic bacteria in aquatic ecosystems, inhabiting a unique ecological niche with significant ecological function, have long been the subject of attention. Habitat characteristics and plant species are believed to be important in controlling the assembly of epiphytic bacteria. However, the underlying principle governing the assembly of the epiphytic bacterial community on macrophytes is far from clear. In this study, we systematically compared the diversity and community composition of epiphytic bacteria both in different habitats and on different species of macrophytes where they were attached. Results suggested that neither the plant species nor the habitat had a significant effect on the diversity and community of epiphytic bacteria independently, indicating that the epiphytic bacterial community composition was correlated to both geographical distance and individual species of macrophytes. Furthermore, almost all of the abundant taxa were shared between different lake regions or macrophyte species, and the most abundant bacteria belonged to Proteobacteria and Firmicutes. Our results demonstrated that the competitive lottery model may explain the pattern of epiphytic bacterial colonization of submerged macrophyte surfaces. This research could provide a new perspective for exploring plant-microbe interaction in aquatic systems and new evidence for the lottery model as the mechanism best explaining the assembly of epiphytic bacteria.

Entry pathways determined the effects of MPs on sludge anaerobic digestion system: The views of methane production and antibiotic resistance genes fates

Sludge is one of the primary reservoirs of microplastics (MPs), and the effects of MPs on subsequent sludge treatment raised attention. Given the entry pathways, MPs would exhibit different properties, but the entry pathway-dependent effect of MPs on sludge treatment performance and the fates of antibiotic resistance genes (ARGs), another high-risk emerging contaminant, were seldom documented. Herein, MPs with two predominant entry pathways, including wastewater-derived (WW-derived) and anaerobic digestion-introduced (AD-introduced), were used to investigate the effects on AD performance and ARGs abundances. The results indicated that WW-derived MPs, namely the MPs accumulated in sludge during the wastewater treatment process, exhibited significant inhibition on methane production by 22.8%-71.6%, while the AD-introduced MPs, being introduced in the sludge AD process, slightly increased the methane yield by 4.7%-17.1%. Meanwhile, MPs were responsible for promoting transmission of target ARGs, and polyethylene terephthalate MPs (PET-MPs) showed a greater promotion effect (0.0154-0.0936) than polyamide MPs (PA-MPs) (0.0013-0.0724). Compared to size, entry pathways and types played more vital roles on MPs influences. Investigation on mechanisms based on microbial community structure revealed characteristics (aging degree and types) of MPs determined the differences of AD performance and ARGs fates. WW-derived MPs with longer aging period and higher aging degree would release toxics and decrease the activities of microorganisms, resulting in the negative impact on AD performance. However, AD-introduced MPs with short aging period exhibited marginal impacts on AD performance. Furthermore, the co-occurrent network analysis suggested that the variations of potential host bacteria induced by MPs with different types and aging degree attributed to the dissemination of ARGs. Distinctively from most previous studies, the MPs with different sizes did not show remarkable effects on AD performance and ARGs fates. Our findings benefited the understanding of realistic environmental behavior and effect of MPs with different sources.

MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters

Anaerobic digestion of organic waste into methane and carbon dioxide (biogas) is carried out by complex microbial communities. Here, we use full-length 16S rRNA gene sequencing of 285 full-scale anaerobic digesters (ADs) to expand our knowledge about diversity and function of the bacteria and archaea in ADs worldwide. The sequences are processed into full-length 16S rRNA amplicon sequence variants (FL-ASVs) and are used to expand the MiDAS 4 database for bacteria and archaea in wastewater treatment systems, creating MiDAS 5. The expansion of the MiDAS database increases the coverage for bacteria and archaea in ADs worldwide, leading to improved genus- and species-level classification. Using MiDAS 5, we carry out an amplicon-based, global-scale microbial community profiling of the sampled ADs using three common sets of primers targeting different regions of the 16S rRNA gene in bacteria and/or archaea. We reveal how environmental conditions and biogeography shape the AD microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 692 genera and 1013 species. These represent 84-99% and 18-61% of the accumulated read abundance, respectively, across samples depending on the amplicon primers used. Finally, we examine the global diversity of functional groups with known importance for the anaerobic digestion process.

Microbial community assembly in engineered bioreactors

Microbial community assembly (MCA) processes that shape microbial communities in environments are being used to analyze engineered bioreactors such as activated sludge systems and anaerobic digesters. The goal of studying MCA is to be able to understand and predict the effect of design and operation procedures on bioreactor microbial composition and function. Ultimately, this can lead to bioreactors that are more efficient, resilient, or resistant to perturbations. This review summarizes the ecological theories underpinning MCA, evaluates MCA analysis methods, analyzes how these MCA-based methods are applied to engineered bioreactors, and extracts lessons from case studies. Furthermore, we suggest future directions in MCA research in engineered bioreactor systems. The review aims to provide insights and guidance to the growing number of environmental engineers who wish to design and understand bioreactors through the lens of MCA.

Microbial community structure in a constructed wetland based on a recirculating aquaculture system: Exploring spatio-temporal variations and assembly mechanisms

The diversity, composition and performance of microbial communities within constructed wetlands (CW) were markedly influenced by spatio-temporal variations. A pilot-scale integrated vertical-flow constructed wetland (IVCW) as the biological purification unit within a recirculating aquaculture system (RAS) was established and monitored in this study. The investigation aimed to elucidate the responses of community structure, co-occurrence networks, and assembly mechanisms of the microbial community to spatial and temporal changes. Spatially, all a-diversity indices and microbial networks complexity were significantly higher in the upstream pool of the IVCW than in the downstream pool. Temporally, the richness increased over time, while the evenness showed a decreasing trend. The number of nodes and edges of microbial networks increased over time. Notably, the stable pollutant removal efficiencies were observed during IVCW operations, despite a-diversity and bacterial community networks exhibited significant variations across time. Functional redundancy emerged as a likely mechanism contributing to the stability of microbial ecosystem functions. Null model and neutral model analyses revealed the dominance of deterministic processes shaping microbial communities over time, with deterministic influences being more pronounced at lower a-diversity levels. DO and inorganic nitrogen emerged as the principal environmental factor influencing microbial community dynamics. This study provides a theoretical foundation for the regulation of microbial communities and environmental factors within the context of IVCW.

Functional Redundant Microbiome Enhanced Anaerobic Digestion Efficiency under Ammonium Inhibition Conditions

Revealing the role of functional redundancy is of great importance considering its key role in maintaining the stability of microbial ecosystems in response to various disturbances. However, experimental evidence on this point is still lacking due to the difficulty in "manipulating" and depicting the degree of redundancy. In this study, manipulative experiments of functional redundancy were conducted by adopting the mixed inoculation strategy to evaluate its role in engineered anaerobic digestion systems under ammonium inhibition conditions. The results indicated that the functional redundancy gradient was successfully constructed and confirmed by evidence from pathway levels. All mixed inoculation groups exhibited higher methane production regardless of the ammonium level, indicating that functional redundancy is crucial in maintaining the system's efficiency. Further analysis of the metagenome-assembled genomes within different functional guilds revealed that the extent of redundancy decreased along the direction of the anaerobic digestion flow, and the role of functional redundancy appeared to be related to the stress level. The study also found that microbial diversity of key functional populations might play a more important role than their abundance on the system's performance under stress. The findings provide direct evidence and highlight the critical role of functional redundancy in enhancing the efficiency and stability of anaerobic digestion.

Temperature-driven carboxylic acid production from waste activated sludge and food waste: Co-fermentation performance and microbial dynamics

This work aims to improve the continuous co-fermentation of waste activated sludge (WAS) and food waste (FW) by investigating the long-term impact of temperature on fermentation performance and the underpinning microbial community. Acidogenic co-fermentation of WAS and FW (70:30 % VS-basis) to produce volatile fatty acids (VFA) was studied in continuous fermenters at different temperatures (25, 35, 45, 55 °C) at an organic loading rate of 11 gVS/(L·d) and a hydraulic retention time of 3.5 days. Two batches of WAS (A and B) were collected from the same wastewater treatment plant at different periods to understand the impact of the WAS microbioota on the fermenters' microbial communities. Solubilisation yield was higher at 45 °C (575 ± 68 mgCOD/gVS) followed by 55 °C (508 ± 45 mgCOD/gVS). Fermentation yield was higher at 55 °C (425 ± 28 mgCOD/gVS) followed by 35 °C (327 ± 17 mgCOD/gVS). Temperature also had a noticeable impact on the VFA profile. At 55 °C, acetic (40 %) and butyric (40 %) acid dominated, while acetic (37 %), butyric acid (31 %), and propionic acid (17 %) dominated at 35 °C. At 45 °C, an accumulation of caproic acid was detected which did not occur at other temperatures. Each temperature had a distinct microbial community, where the WAS microbiota played an important role. The biomass mass-balance showed the highest growth of microorganisms (51 %) at 35 °C and WAS_B, where a consumption of acetic acid was observed. Therefore, at 35 °C, there is a higher risk of acetic acid consumption probably due to the proliferation of methanogens imported from WAS.

Nitrogen deposition mediates more stochastic processes in structuring plant community than soil microbial community in the Eurasian steppe

Anthropogenic environmental changes may affect community assembly through mediating both deterministic (e.g., competitive exclusion and environmental filtering) and stochastic processes (e.g., birth/death and dispersal/colonization). It is traditionally thought that environmental changes have a larger mediation effect on stochastic processes in structuring soil microbial community than aboveground plant community; however, this hypothesis remains largely untested. Here we report an unexpected pattern that nitrogen (N) deposition has a larger mediation effect on stochastic processes in structuring plant community than soil microbial community (those <2 mm in diameter, including archaea, bacteria, fungi, and protists) in the Eurasian steppe. We performed a ten-year nitrogen deposition experiment in a semiarid grassland ecosystem in Inner Mongolia, manipulating nine rates (0-50 g N m-2 per year) at two frequencies (nitrogen added twice or 12 times per year) under two grassland management strategies (fencing or mowing). We separated the compositional variation of plant and soil microbial communities caused by each treatment into the deterministic and stochastic components with a recently-developed method. As nitrogen addition rate increased, the relative importance of stochastic component of plant community first increased and then decreased, while that of soil microbial community first decreased and then increased. On the whole, the relative importance of stochastic component was significantly larger in plant community (0.552±0.035; mean±standard error) than in microbial community (0.427±0.035). Consistently, the proportion of compositional variation explained by the deterministic soil and community indices was smaller for plant community (0.172-0.186) than microbial community (0.240-0.767). Meanwhile, as nitrogen addition rate increased, the linkage between plant and microbial community composition first became weaker and then became stronger. The larger stochasticity in plant community relative to microbial community assembly suggested that more stochastic strategies (e.g., seeds addition) should be adopted to maintain above- than below-ground biodiversity under the pressure of nitrogen deposition.

Analysis of the differences in physicochemical properties, volatile compounds, and microbial community structure of pit mud in different time spaces

Pit mud (PM) is among the key factors determining the quality of Nongxiangxing baijiu, a Chinese liquor. Microorganisms present inside PM are crucial for the unique taste and flavor of this liquor. In this study, headspace solid-phase microextraction was used in combination with gas chromatography and high-throughput sequencing to determine the volatile compounds and microbial community structure of 10- and 40-year PM samples from different spaces. The basic physicochemical properties of the PM were also determined. LEfSe and RDA were used to systematically study the PM in different time spaces. The physicochemical properties and ester content of the 40-year PM were higher than those of the 10-year PM, but the spatial distribution of the two years PM samples exhibited no consistency, except in terms of pH, available phosphorus content, and ester content. In all samples, 29 phyla, 276 families, and 540 genera of bacteria, including four dominant phyla and 20 dominant genera, as well as eight phyla, 24 families, and 34 genera of archaea, including four dominant phyla and seven dominant genera, were identified. The LEfSe analysis yielded 18 differential bacteria and five differential archaea. According to the RDA, the physicochemical properties and ethyl caproate, ethyl octanoate, hexanoic acid, and octanoic acid positively correlated with the differential microorganisms of the 40-year PM, whereas negatively correlated with the differential microorganisms of the 10-year PM. Thus, we inferred that Caproiciproducens, norank_f__Caloramatoraceae, and Methanobrevibacter play a dominant and indispensable role in the PM. This study systematically unveils the differences that affect the quality of PM in different time spaces and offers a theoretical basis for improving the declining PM, promoting PM aging, maintaining cellars, and cultivating an artificial PM at a later stage.

Syntrophic microbes involved in the oxidation of short-chain fatty acids in continuous-flow anaerobic digesters treating waste activated sludge with hydrochar

The rapid degradation of short-chain fatty acids (SCFAs) is an essential issue of anaerobic digestion (AD), in which SCFA oxidizers could generally metabolize in syntrophy with methanogens. The dynamic responses of active metagenome-assembled genomes to low concentrations of propionate and acetate were analyzed to identify specific syntrophic SCFA oxidizers and their metabolic characteristics in continuous-flow AD systems treating waste activated sludge with and without hydrochar. In this study, hydrochar increased methane production by 19%, possibly due to hydrochar enhancing acidification and methanogenesis processes. A putative syntrophic propionate oxidizer and two acetate oxidizers contributed substantially to the syntrophic degradation of SCFAs, and hydrochar positively regulated their functional gene expressions. A significant relationship was established between the replication rate of SCFA oxidizers and their stimulation-related transcriptional activity. Acetate was degraded in the hydrochar group, which might be mainly through the syntrophic acetate oxidizer from the genus Desulfallas and methanogens from the genus Methanosarcina.IMPORTANCEShort-chain fatty acid (SCFA) degradation is an important process in the methanogenic ecosystem. However, current knowledge of this microbial mechanism is mainly based on studies on a few model organisms incubated as mono- or co-cultures or in enrichments, which cannot provide appropriate evidence in complex environments. Here, this study revealed the microbial mechanism of a hydrochar-mediated anaerobic digestion (AD) system promoting SCFA degradation at the species level and identified key SCFA oxidizing bacteria. Our analysis provided new insights into the SCFA oxidizers involved in the AD of waste activated sludge facilitated by hydrochar.

Stochastic Assembly Increases the Complexity and Stability of Shrimp Gut Microbiota During Aquaculture Progression

The gut microbiota of aquaculture species contributes to their food metabolism and regulates their health, which has been shown to vary during aquaculture progression of their hosts. However, limited research has examined the outcomes and mechanisms of these changes in the gut microbiota of hosts. Here, Kuruma shrimps from the beginning, middle, and late stages of aquaculture progression (about a time duration of 2 months between each stage) were collected and variations in the gut microbiota of Kuruma shrimp during the whole aquaculture process were examined. High-throughput sequencing demonstrated increases in the diversity and richness of the shrimp gut microbiota with aquaculture progression. In addition, the gut microbiota composition differed among cultural stages, with enrichment of Firmicutes, RF39, and Megamonas and a reduction in Proteobacteria in the mid-stage. Notably, only very few taxa were persistent in the shrimp gut microbiota during the whole aquaculture progression, while the number of taxa that specific to the end of aquaculture was high. Network analysis revealed increasing complexity of the shrimp gut microbiota during aquaculture progression. Moreover, the shrimp gut microbiota became significantly more stable towards the end of aquaculture. According to the results of neutral community model, contribution of stochastic processes for shaping the shrimp gut microbiota was elevated along the aquaculture progression. This study showed substantial variations in shrimp gut microbiota during aquaculture progression and explored the underlying mechanisms regulating these changes.

Efficacy of bioaugmentation with nondomesticated mixed microbial consortia under ammonia inhibition in anaerobic digestion

Bioaugmentation shows promise in mitigating ammonia-induced microbial inhibition in anaerobic digestion processes. However, the advanced technical requirements and high costs associated with pure strain cultivation, as well as the time-consuming and labor-intensive process of domesticating consortia, present challenges for industrial applications. Herein, the efficacy of bioaugmentation with nondomesticated mixed microbial consortia was evaluated, which resulted in a significant methane production improvement of 5.6%-11.7% and 10.3%-13.5% under total ammonia nitrogen concentrations of 2.0 and 4.9 g-N/L, respectively. Microbial analysis revealed that at high ammonium levels, the bioaugmented culture facilitated a transition in the methanogenic pathway from acetoclastic to hydrogenotrophic by regulating symbiotic relationships between propionate- and acetate-oxidizing bacteria and methanogens. Consortium type and dose applied were identified as crucial factors determining bioaugmentation effectiveness. Overall, nondomesticated mixed microbial consortia demonstrate potential as cost-effective bioaugmentation agents for mitigating ammonia-induced inhibition.

Resistance of aerobic granular sludge microbiomes to periodic loss of biomass

Granular sludge is a biofilm process used for wastewater treatment which is currently being implemented worldwide. It is important to understand how disturbances affect the microbial community and performance of reactors. Here, two acetate-fed replicate reactors were inoculated with acclimatized sludge and the reactor performance, and the granular sludge microbial community succession were studied for 149 days. During this time, the microbial community was challenged by periodically removing half of the reactor biomass, subsequently increasing the food-to-microorganism (F/M) ratio. Diversity analysis together with null models show that overall, the microbial communities were resistant to the disturbances, observing some minor effects on polyphosphate-accumulating and denitrifying microbial communities and their associated reactor functions. Community turnover was driven by drift and random granule loss, and stochasticity was the governing ecological process for community assembly. These results evidence the aerobic granular sludge process as a robust system for wastewater treatment.

Resilience and functional redundancy of methanogenic digestion microbiome safeguard recovery of methanogenesis activity under the stress induced by microplastics

Microplastics and nanoplastics are emerging pollutants that substantially influence biological element cycling in natural ecosystems. Plastics are also prevalent in sewage, and they accumulate in waste-activated sludge (WAS). However, the impacts of plastics on the methanogenic digestion of WAS and the underpinning microbiome remain underexplored, particularly during long-term operation. In this study, we found that short-term exposure to individual microplastics and nanoplastics (polyethylene, polyvinyl chloride, polystyrene, and polylactic acid) at a low concentration (10 particles/g sludge) slightly enhanced methanogenesis by 2.1%-9.0%, whereas higher levels (30-200 particles/g sludge) suppressed methanogenesis by 15.2%-30.1%. Notably, the coexistence of multiple plastics, particularly at low concentrations, showed synergistic suppression of methanogenesis. Unexpectedly, methanogenesis activity completely recovered after long-term exposure to plastics, despite obvious suppression of methanogenesis by initial plastic exposure. The inhibition of methanogenesis by plastics could be attributed to the stimulated generation of reactive oxygen species. The stress induced by plastics dramatically decreased the relative abundance of methanogens but showed marginal influence on putative hydrolytic and fermentation populations. Nonetheless, the digestion sludge microbiome exhibited resilience and functional redundancy, contributing to the recovery of methanogenesis during the long-term operation of digesters. Plastics also increased the complexity, modularity, and negative interaction ratios of digestion sludge microbiome networks, but their influence on community assembly varied. Interestingly, a unique plastisphere was observed, the networks and assembly of which were distinct from the sludge microbiome. Collectively, the comprehensive evaluation of the influence of microplastics and nanoplastics on methanogenic digestion, together with the novel ecological insights, contribute to better understanding and manipulating this engineered ecosystem in the face of increasing plastic pollution.

Succession and assembly mechanisms of seawater prokaryotic communities along an extremely wide salinity gradient

Salinity is an important environmental factor in microbial ecology for affecting the microbial communities in diverse environments. Understanding the salinity adaptation mechanisms of a microbial community is a significant issue, while most previous studies only covered a narrow salinity range. Here, variations in seawater prokaryotic communities during the whole salt drying progression (salinity from 3% to 25%) were investigated. According to high-throughput sequencing results, the diversity, composition, and function of seawater prokaryotic communities varied significantly along the salinity gradient, expressing as decreased diversity, enrichment of some halophilic archaea, and powerful nitrate reduction in samples with high salt concentrations. More importantly, a sudden and dramatic alteration of prokaryotic communities was observed when salinity reached 16%, which was recognized as the change point. Combined with the results of network analysis, we found the increasing of complexity but decreasing of stability in prokaryotic communities when salinity exceeded the change point. Moreover, prokaryotic communities became more deterministic when salinity exceeded the change point due to the niche adaptation of halophilic species. Our study showed that substantial variations in seawater prokaryotic communities along an extremely wide salinity gradient, and also explored the underlying mechanisms regulating these changes.

Influence of phycospheric bacterioplankton disruption or removal on algae growth and survival

Phycospheric bacteria play a crucial role in the survival of microalgae. However, the potential of using the growth regulation and community structure modulation of phycospheric bacteria to prevent the occurrence of blooms is yet to be verified. The phycospheric bacterioplankton of Cyclotella sp. can be categorized into HNA (high nucleic acid) bacteria and LNA (low nucleic acid) bacteria. 16S rRNA sequencing showed that the HNA bacteria exhibited higher α-diversity compared to the LNA bacteria, and the microbial community composition also exhibited variations. Metagenomic sequencing further indicated the distinct ecological functions between HNA and LNA bacteria. Furthermore, the study showcased the restorative capacity of the phycospheric bacterioplankton. Biomass analysis revealed that the recovery of phycospheric bacterioplankton positively influenced the microalgae growth, thus affirming the significance of phycospheric bacterioplankton to microalgae. The community structure of phycospheric bacterioplankton demonstrated a notable decrease in the abundance of restored LNA core bacteria. Additionally, the restored phycospheric bacterioplankton exhibited a more complex co-occurrence network structure, resulting in decreased resistance and sensitivity of microalgae to adverse environments. The presence of phycospheric bacterioplankton provides a protective shield for microalgae, and thus destabilizing or removing phycospheric bacterioplankton may effectively inhibit growth of microalgae.

Statistically learning the functional landscape of microbial communities

Microbial consortia exhibit complex functional properties in contexts ranging from soils to bioreactors to human hosts. Understanding how community composition determines function is a major goal of microbial ecology. Here we address this challenge using the concept of community-function landscapes-analogues to fitness landscapes-that capture how changes in community composition alter collective function. Using datasets that represent a broad set of community functions, from production/degradation of specific compounds to biomass generation, we show that statistically inferred landscapes quantitatively predict community functions from knowledge of species presence or absence. Crucially, community-function landscapes allow prediction without explicit knowledge of abundance dynamics or interactions between species and can be accurately trained using measurements from a small subset of all possible community compositions. The success of our approach arises from the fact that empirical community-function landscapes appear to be not rugged, meaning that they largely lack high-order epistatic contributions that would be difficult to fit with limited data. Finally, we show that this observation holds across a wide class of ecological models, suggesting community-function landscapes can be efficiently inferred across a broad range of ecological regimes. Our results open the door to the rational design of consortia without detailed knowledge of abundance dynamics or interactions.

Effect of mixing intensity on volatile fatty acids production in sludge alkaline fermentation: Insights from dissolved organic matter characteristics and functional microorganisms

Alkaline fermentation for volatile fatty acids (VFAs) production has shown potential as a viable approach to treat sewage sludge. The hydrolysis and acidogenesis of sludge are greatly influenced by mixing. However, the effects of mixing intensity on VFAs production in sludge alkaline fermentation (SAF) remain poorly understood. This study investigated the impacts of mixing intensity (30, 90 and 150 rpm continuous mixing, and 150 rpm intermittent mixing) on VFAs production, dissolved organic matter (DOM) characteristics, phospholipid fatty acid profiles and microbial population distribution in SAF. Results showed that 150 rpm continuous and intermittent mixing enhanced the hydrolysis of sludge, while 150 rpm intermittent mixing resulted in the highest VFAs production (3886 ± 266.1 mg COD/L). Analysis of fluorescent and molecular characteristics of DOM revealed that 150 rpm intermittent mixing facilitated the conversion of released DOM, especially proteins-like substances, into VFAs. The abundance of unsaturated and branched fatty acids of microbes increased under 150 rpm intermittent mixing, which could aid in DOM degradation and VFAs production. Firmicutes and Tissierella were enriched at 150 rpm intermittent mixing, which favored the maximum VFAs yield. Moreover, Firmicutes were found to be the key functional microorganisms influencing the yield of VFAs during SAF. This study provides an understanding about the mixing intensity effects on VFAs production during SAF, which could be helpful to improve the yield of VFAs.

Soil salinity is the main factor influencing the soil bacterial community assembly process under long-term drip irrigation in Xinjiang, China

Identifying the potential factors associated with the impact of long-term drip irrigation (DI) on soil ecosystems is essential for responding to the environmental changes induced by extensive application of DI technology in arid regions. Herein, we examined the effects of the length of time that DI lasts in years (NDI) on soil bacterial diversity as well as the soil bacterial community assembly process and the factors influencing it. The results showed that long-term DI substantially reduced soil salinity and increased soil bacterial diversity while affecting the soil bacterial community structure distinctly. Null model results showed that the soil bacterial community assembly transitioned from stochastic processes to deterministic processes, as NDI increased. Homogeneous selection, a deterministic process, emerged as the dominant process when NDI exceeded 15 years. Both random forest and structural equation models showed that soil salinity was the primary factor affecting the bacterial community assembly process. In summary, this study suggested that soil bacteria respond differently to long-term DI and depends on the NDI, influencing the soil bacterial community assembly process under long-term DI.

Microbial biogeography of pit mud from an artificial brewing ecosystem on a large time scale: all roads lead to Rome

IMPORTANCE

Baijiu is a typical example of how humans employ microorganisms to convert grains into new flavors. Mud cellars are used as the fermentation vessel for strong-flavor Baijiu (SFB) to complete the decomposition process of grains. The typical flavor of SFB is mainly attributed to the metabolites of the pit mud microbiome. China has a large number of SFB-producing regions. Previous research revealed the temporal profiles of the pit mud microbiome in different geographical regions. However, each single independent study rarely yields a thorough understanding of the pit mud ecosystem. Will the pit mud microbial communities in different production regions exhibit similar succession patterns and structures under the impact of the brewing environment? Hence, we conducted research in pit mud microbial biogeography to uncover the impact of specific environment on the microbial community over a long time scale.

Unraveling antibiotic resistomes associated with bacterial and viral communities in intertidal mudflat aquaculture area

The extensive use of antibiotics in intertidal mudflat aquaculture area has substantially increased the dissemination risk of antibiotic resistance genes (ARGs). As hosts of ARGs, bacteria and virus exert vital effects on ARG dissemination. However, the insights for the interrelationships among ARGs, bacteria, and virus have not been thoroughly explored in intertidal mudflat. Therefore, this study attempts to unravel the occurrence, dissemination, evolution, and driving mechanisms of ARGs associated with bacterial and viral communities using metagenomic sequencing in a typical intertidal mudflat. Abundant and diverse ARGs (22 types and 437 subtypes) were identified and those of ARGs were higher in spring than in autumn. It is worthy noted that virus occupied a more essential position than bacteria for ARGs dissemination through network analysis. Meanwhile, nitrogen exerted indirect effect on ARG profiles by shaping viral and bacterial diversity. According to the results of neutral and null models, deterministic processes dominated the ARG community assembly by controlling sediment nitrogen and antibiotics. Homogeneous and variable selection dominated phylogenetic turnover of ARG community, contributing 46.15% and 45.90% of the total processes, respectively. This study can hence theoretically support for the ARG pollution control and management in intertidal mudflat aquaculture area.

Seasonal variations in acidogenic fermentation of filter primary sludge

Primary treatment of municipal wastewater by rotating belt filtration followed by hydrolysis and acidogenic fermentation of the filter primary sludge (FPS) at ambient temperature was studied at pilot-scale during one year. The seasonal variations of volatile fatty acids (VFAs), nutrient release and soluble COD production as well as microbial community assembly were assessed, leading to novel findings for fermentation at ambient temperature. The reproducibility of VFA production performance was first established by operating the two fermentation reactors under the same conditions, showing similar results regarding VFA production and microbial community structure. One year of operation at 5 d retention time (RT) and 16-29 °C resulted in an average VFA yield of 180±35 mg COD/g VSin and soluble COD yield of 242±40 mg COD/g VSin. The VFA formation was temperature-dependent, with ϴ=1.033±0.005 ( [Formula: see text] . The seasonal variations of the acetic and propionic acid productions were pronounced, whereas the productions of VFAs with longer chains were more stable regardless of temperature. The community structure of the reactor microbiomes was also clearly affected by season and temperature and linked with the production spectrum of VFAs. The ammonium and phosphate releases were stable during the year, leading to a decrease in ratios of soluble COD to NH4+-N and PO43--P during winter. The soluble COD yield was 11% and 27% higher at 5 d RT compared to 3 and 2 d RT respectively, but the corresponding volumetric productivities were lower. The dissimilarities between microbiomes in influent FPS and fermenters were significant even at a short RT of 2 d, and increased with longer RT of 3 and 5 d, primarily caused by selection of bacteria within Bacteroidota in the fermentation reactors.

Inter-kingdom interactions and stability of methanogens revealed by machine-learning guided multi-omics analysis of industrial-scale biogas plants

Multi-omics analysis is a powerful tool for the detection and study of inter-kingdom interactions, such as those between bacterial and archaeal members of complex biogas-producing microbial communities. In the present study, the microbiomes of three industrial-scale biogas digesters, each fed with different substrates, were analysed using a machine-learning guided genome-centric metagenomics framework complemented with metatranscriptome data. This data permitted us to elucidate the relationship between abundant core methanogenic communities and their syntrophic bacterial partners. In total, we detected 297 high-quality, non-redundant metagenome-assembled genomes (nrMAGs). Moreover, the assembled 16 S rRNA gene profiles of these nrMAGs showed that the phylum Firmicutes possessed the highest copy number, while the representatives of the archaeal domain had the lowest. Further investigation of the three anaerobic microbial communities showed characteristic alterations over time but remained specific to each industrial-scale biogas plant. The relative abundance of various microorganisms as revealed by metagenome data was independent from corresponding metatranscriptome activity data. Archaea showed considerably higher activity than was expected from their abundance. We detected 51 nrMAGs that were present in all three biogas plant microbiomes with different abundances. The core microbiome correlated with the main chemical fermentation parameters, and no individual parameter emerged as a predominant shaper of community composition. Various interspecies H₂/electron transfer mechanisms were assigned to hydrogenotrophic methanogens in the biogas plants that ran on agricultural biomass and wastewater. Analysis of metatranscriptome data revealed that methanogenesis pathways were the most active of all main metabolic pathways.

Accurate prediction of huanglongbing occurrence in citrus plants by machine learning-based analysis of symbiotic bacteria

Huanglongbing (HLB), the most prevalent citrus disease worldwide, is responsible for substantial yield and economic losses. Phytobiomes, which have critical effects on plant health, are associated with HLB outcomes. The development of a refined model for predicting HLB outbreaks based on phytobiome markers may facilitate early disease detection, thus enabling growers to minimize damages. Although some investigations have focused on differences in the phytobiomes of HLB-infected citrus plants and healthy ones, individual studies are inappropriate for generating common biomarkers useful for detecting HLB on a global scale. In this study, we therefore obtained bacterial information from several independent datasets representing hundreds of citrus samples from six continents and used these data to construct HLB prediction models based on 10 machine learning algorithms. We detected clear differences in the phyllosphere and rhizosphere microbiomes of HLB-infected and healthy citrus samples. Moreover, phytobiome alpha diversity indices were consistently higher for healthy samples. Furthermore, the contribution of stochastic processes to citrus rhizosphere and phyllosphere microbiome assemblies decreased in response to HLB. Comparison of all constructed models indicated that a random forest model based on 28 bacterial genera in the rhizosphere and a bagging model based on 17 bacterial species in the phyllosphere predicted the health status of citrus plants with almost 100% accuracy. Our results thus demonstrate that machine learning models and phytobiome biomarkers may be applied to evaluate the health status of citrus plants.

Niche Modification by Sulfate-Reducing Bacteria Drives Microbial Community Assembly in Anoxic Marine Sediments

Sulfate-reducing bacteria (SRB) are essential functional microbial taxa for degrading organic matter (OM) in anoxic marine environments. However, there are little experimental data regarding how SRB regulates microbial communities. Here, we applied a top-down microbial community management approach by inhibiting SRB to elucidate their contributions to the microbial community during OM degradation. Based on the highly replicated microcosms (n = 20) of five different incubation stages, we found that many microbial community properties were influenced after inhibiting SRB, including the composition, structure, network, and community assembly processes. We also found a strong coexistence pattern between SRB and other abundant phylogenetic lineages via positive frequency-dependent selection. The relative abundances of the families Synergistaceae, Peptostreptococcaceae, Dethiosulfatibacteraceae, Prolixibacteraceae, Marinilabiliaceae, and Marinifilaceae were simultaneously suppressed after inhibiting SRB during OM degradation. A close association between SRB and the order Marinilabiliales among coexisting taxa was most prominent. They contributed to preserved modules during network successions, were keystone nodes mediating the networked community, and contributed to homogeneous ecological selection. The molybdate tolerance test of the isolated strains of Marinilabiliales showed that inhibited SRB (not the inhibitor of SRB itself) triggered a decrease in the relative abundance of Marinilabiliales. We also found that inhibiting SRB resulted in reduced pH, which is unsuitable for the growth of most Marinilabiliales strains, while the addition of pH buffer (HEPES) in SRB-inhibited treatment microcosms restored the pH and the relative abundances of these bacteria. These data supported that SRB could modify niches to affect species coexistence. IMPORTANCE Our model offers insight into the ecological properties of SRB and identifies a previously undocumented dimension of OM degradation. This targeted inhibition approach could provide a novel framework for illustrating how functional microbial taxa associate the composition and structure of the microbial community, molecular ecological network, and community assembly processes. These findings emphasize the importance of SRB during OM degradation. Our results proved the feasibility of the proposed study framework, inhibiting functional taxa at the community level, for illustrating when and to what extent functional taxa can contribute to ecosystem services.

The ecology of bacterial communities in groundwater of industrial areas: Diversity, composition, network, and assembly

Groundwater provides freshwater resources necessary for mankind, but its quality is significantly impacted by anthropologic activities. The unique characteristics of groundwater provide a special niche for bacterial colonization. To maintain the sustainability of groundwater ecosystem, a good understanding of the influencing factors and assembly mechanisms for bacterial communities is necessary. Here, we investigated the bacterial communities of groundwater from two industrial zones in Shanghai, a highly industrialized city, during the wet and dry seasons using the high-throughput sequencing technology. Our study uncovered the significant effects of season, geographical location, and industrial type on the diversity and composition of groundwater bacterial communities, particularly, we found that season was the most dominant factor with much stronger influences (give the explanation 17.7%) in comparison with geographical location (8.8%) and industrial type (7.5%). Co-occurrence networks revealed that geographical location explained more variations of bacterial ecological network than season did. Both distance-decay of similarities and variation partitioning analyses indicated that the assembly of groundwater bacterial communities was more governed by environmental filtering compared to spatial-related dispersal. Finally, null model analysis suggested the role of stochastic processes, including dispersal and drift, in shaping the groundwater bacterial communities cannot be ignored. These findings would benefit to improve our understanding of the bacterial communities in groundwater ecosystem and provide a theoretical foundation for groundwater health management.

Deterministic Assembly Processes Strengthen the Effects of β-Diversity on Community Biomass of Marine Bacterioplankton

The presence of more species in the community of a sampling site (α diversity) typically increases ecosystem functions via nonrandom processes like resource partitioning. When considering multiple communities, we hypothesize that higher compositional difference (β diversity) increases overall functions of these communities. Further, we hypothesize that the β diversity effect is more positive when β diversity is increased by nonrandom assembly processes. To test these hypotheses, we collected bacterioplankton along a transect of 6 sampling sites in the southern East China Sea in 14 cruises. For any pairs of the 6 sites within a cruise, we calculated the Bray-Curtis index to represent β diversity and summed bacterial biomass as a proxy to indicate the overall function of the two communities. We then calculated deviation of observed mean pairwise phylogenetic similarities among species in two communities from random to represent the influences of nonrandom processes. The bacterial β diversity was found to positively affect the summed bacterial biomass; however, the effect varied among cruises. Cross-cruise comparison indicated that the β diversity effect increased with the nonrandom processes selecting for phylogenetically dissimilar species. This study extends biodiversity-ecosystem functioning research to the scale of multiple sites and enriches the framework by considering community assembly processes. IMPORTANCE The implications of our analyses are twofold. First, we emphasize the importance of studying β diversity. We expanded the current biodiversity-ecosystem functioning framework from single to multiple sampling sites and investigated the influences of species compositional differences among sites on the overall functioning of these sites. Since natural ecological communities never exist alone, our analyses allow us to more holistically perceive the role of biodiversity in natural ecosystems. Second, we took community assembly processes into account to attain a more mechanistic understanding of the impacts of biodiversity on ecosystem functioning.

Metagenomic Analysis of Anaerobic Microbial Communities Degrading Short-Chain Fatty Acids as Sole Carbon Sources

Analyzing microbial communities using metagenomes is a powerful approach to understand compositional structures and functional connections in anaerobic digestion (AD) microbiomes. Whereas short-read sequencing approaches based on the Illumina platform result in highly fragmented metagenomes, long-read sequencing leads to more contiguous assemblies. To evaluate the performance of a hybrid approach of these two sequencing approaches we compared the metagenome-assembled genomes (MAGs) resulting from five AD microbiome samples. The samples were taken from reactors fed with short-chain fatty acids at different feeding regimes (continuous and discontinuous) and organic loading rates (OLR). Methanothrix showed a high relative abundance at all feeding regimes but was strongly reduced in abundance at higher OLR, when Methanosarcina took over. The bacterial community composition differed strongly between reactors of different feeding regimes and OLRs. However, the functional potential was similar regardless of feeding regime and OLR. The hybrid sequencing approach using Nanopore long-reads and Illumina MiSeq reads improved assembly statistics, including an increase of the N50 value (on average from 32 to 1740 kbp) and an increased length of the longest contig (on average from 94 to 1898 kbp). The hybrid approach also led to a higher share of high-quality MAGs and generated five potentially circular genomes while none were generated using MiSeq-based contigs only. Finally, 27 hybrid MAGs were reconstructed of which 18 represent potentially new species-15 of them bacterial species. During pathway analysis, selected MAGs revealed similar gene patterns of butyrate degradation and might represent new butyrate-degrading bacteria. The demonstrated advantages of adding long reads to metagenomic analyses make the hybrid approach the preferable option when dealing with complex microbiomes.

Continuous irregular dynamics with multiple neutral trajectories permit species coexistence in competitive communities

The colonization model formulates competition among propagules for habitable sites to colonize, which serves as a mechanism enabling coexistence of multiple species. This model traditionally assumes that encounters between propagules and sites occur as mass action events, under which species distribution can eventually reach an equilibrium state with multiple species in a constant environment. To investigate the effects of encounter mode on species diversity, we analyzed community dynamics in the colonization model by varying encounter processes. The analysis indicated that equilibrium is approximately neutrally-stable under perfect ratio-dependent encounter, resulting in temporally continuous variation of species' frequencies with irregular trajectories even under a constant environment. Although the trajectories significantly depend on initial conditions, they are considered to be "strange nonchaotic attractors" (SNAs) rather than chaos from the asymptotic growth rates of displacement. In addition, trajectories with different initial conditions remain different through time, indicating that the system involves an infinite number of SNAs. This analysis presents a novel mechanism for transient dynamics under competition.

Linking human impacts to community processes in terrestrial and freshwater ecosystems

Human impacts such as habitat loss, climate change and biological invasions are radically altering biodiversity, with greater effects projected into the future. Evidence suggests human impacts may differ substantially between terrestrial and freshwater ecosystems, but the reasons for these differences are poorly understood. We propose an integrative approach to explain these differences by linking impacts to four fundamental processes that structure communities: dispersal, speciation, species-level selection and ecological drift. Our goal is to provide process-based insights into why human impacts, and responses to impacts, may differ across ecosystem types using a mechanistic, eco-evolutionary comparative framework. To enable these insights, we review and synthesise (i) how the four processes influence diversity and dynamics in terrestrial versus freshwater communities, specifically whether the relative importance of each process differs among ecosystems, and (ii) the pathways by which human impacts can produce divergent responses across ecosystems, due to differences in the strength of processes among ecosystems we identify. Finally, we highlight research gaps and next steps, and discuss how this approach can provide new insights for conservation. By focusing on the processes that shape diversity in communities, we aim to mechanistically link human impacts to ongoing and future changes in ecosystems.

Community assembly patterns and processes of microbiome responses to habitats and Mytilopsis sallei invasion in the tidal zones of the Pearl River Estuary

The sustainability of estuarine ecosystem functions depends on the stabilization of microbial ecological processes. However, due to the unique and variable habitat characteristics of estuarine areas, in-depth studies on ecological processes such as the spatial distribution and assembly patterns of microbial community structure are lacking. As methods to elucidate this structure, we used 16S rDNA, 18S rDNA and ITS sequencing technologies to study the composition, diversity, spatial pattern and aggregation mechanism of the bacterial, protist and fungal communities in the tidal zones of the Pearl River Estuary (PRETZ). The abundance of bacterial communities was much higher than that of protists and fungi, and the spatial pattern was obvious in PRETZ. The application of neutral and null models revealed the assembly process of three microbial communities dominated by stochastic processes. Among the stochastic processes, undominated processes (64.03 %, 62.45 %, and 59.29 %) were the most critical processes in the assembly of bacterial, fungal and protist communities. Meanwhile, environmental variables, geographic locations, and biological factors were associated with the composition and assembly of bacterial, protist, and fungal communities. Among the environmental variables, dissolved oxygen and salinity were the main predictors that jointly affected the differences in the community structure of the three microorganisms, and geographic location was the second predictor affecting the community structure of the three microorganisms and had a more pronounced effect on the diversity and network structure of the bacterial and fungal communities. However, biological factors exerted a weaker effect on the microbial community structure than spatial factors and only affected bacteria and protists; the invasive species Mytilopsis sallei only affected the process of protist community assembly. In addition, environmental variables affected the relative importance of stochastic processes. In summary, the formation of microbial communities in the PRETZ was affected by random processes, environmental variables, geographic location, and invasive species.

Temporal Succession of Bacterial Community Structure, Co-occurrence Patterns, and Community Assembly Process in Epiphytic Biofilms of Submerged Plants in a Plateau Lake

In shallow macrophytic lakes, epiphytic biofilms are formed on the surface of submerged plant stems and leaves because of algae and bacterial accumulation. Epiphytic biofilms significantly impact the health of the host vegetation and the biogeochemical cycling of lake elements. However, community diversity, species interactions, and community assembly mechanisms in epiphytic bacterial communities (EBCs) of plants during different growth periods are not well understood. We investigated the successional dynamics, co-occurrence patterns, and community assembly processes of epiphytic biofilm bacterial communities of submerged plants, Najas marina and Potamogeton lucens, from July to November 2020. The results showed a significant seasonal variation in EBC diversity and richness. Community diversity and richness increased from July to November, and the temperature was the most important driving factor for predicting seasonal changes in EBC community structure. Co-occurrence network analysis revealed that the average degree and graph density of the network increased from July to November, indicating that the complexity of the EBC network increased. The bacterial community co-occurrence network was limited by temperature, pH, and transparency. The phylogeny-based null model analysis showed that deterministic processes dominated the microbial community assembly in different periods, increasing their contribution. In addition, we found that as the dominance of deterministic processes increased, the microbial co-occurrence links increased, and the potential interrelationships between species became stronger. Thus, the findings provide insights into the seasonal variability of EBC assemblage and co-occurrence patterns in lacustrine ecosystems.

Ecological landscapes guide the assembly of optimal microbial communities

Assembling optimal microbial communities is key for various applications in biofuel production, agriculture, and human health. Finding the optimal community is challenging because the number of possible communities grows exponentially with the number of species, and so an exhaustive search cannot be performed even for a dozen species. A heuristic search that improves community function by adding or removing one species at a time is more practical, but it is unknown whether this strategy can discover an optimal or nearly optimal community. Using consumer-resource models with and without cross-feeding, we investigate how the efficacy of search depends on the distribution of resources, niche overlap, cross-feeding, and other aspects of community ecology. We show that search efficacy is determined by the ruggedness of the appropriately-defined ecological landscape. We identify specific ruggedness measures that are both predictive of search performance and robust to noise and low sampling density. The feasibility of our approach is demonstrated using experimental data from a soil microbial community. Overall, our results establish the conditions necessary for the success of the heuristic search and provide concrete design principles for building high-performing microbial consortia.

Denitrifying anaerobic methane-oxidizing bacteria in river networks of the Taihu Basin: Community dynamics and assembly process

Denitrifying anaerobic methane-oxidizing bacteria (DAMO bacteria) plays an important role in reducing methane emissions from river ecosystems. However, the assembly process of their communities underlying different hydrologic seasons remains unclarified. In this study, the dynamics of DAMO bacterial communities in river networks of the Taihu Basin were investigated by amplicon sequencing across wet, normal, and dry seasons followed by multiple statistical analyses. Phylogenetic analysis showed that Group B was the major subgroup of DAMO bacteria and significant dynamics for their communities were observed across different seasons (constrained principal coordinate analysis, p = 0.001). Furthermore, the neutral community model and normalized stochasticity ratio model were applied to reveal the underlying assembly process. Stochastic process and deterministic process dominated the assembly process in wet season and normal season, respectively and similar contributions of deterministic and stochastic processes were observed in dry season. Meanwhile, abundant (relative abundance >0.1%) and rare (relative abundance <0.01%) DAMO bacterial communities were found to be shaped via distinct assembly processes. Deterministic and stochastic processes played a considerable role in shaping abundant DAMO bacterial communities, while deterministic process mainly shaped rare DAMO bacterial communities. Results of this study revealed the dynamics of DAMO bacterial communities in river networks and provided a theoretical basis for further understanding of the assembly process.

The role of microbial ecology in improving the performance of anaerobic digestion of sewage sludge

The use of next-generation diagnostic tools to optimise the anaerobic digestion of municipal sewage sludge has the potential to increase renewable natural gas recovery, improve the reuse of biosolid fertilisers and help operators expand circular economies globally. This review aims to provide perspectives on the role of microbial ecology in improving digester performance in wastewater treatment plants, highlighting that a systems biology approach is fundamental for monitoring mesophilic anaerobic sewage sludge in continuously stirred reactor tanks. We further highlight the potential applications arising from investigations into sludge ecology. The principal limitation for improvements in methane recoveries or in process stability of anaerobic digestion, especially after pre-treatment or during co-digestion, are ecological knowledge gaps related to the front-end metabolism (hydrolysis and fermentation). Operational problems such as stable biological foaming are a key problem, for which ecological markers are a suitable approach. However, no biomarkers exist yet to assist in monitoring and management of clade-specific foaming potentials along with other risks, such as pollutants and pathogens. Fundamental ecological principles apply to anaerobic digestion, which presents opportunities to predict and manipulate reactor functions. The path ahead for mapping ecological markers on process endpoints and risk factors of anaerobic digestion will involve numerical ecology, an expanding field that employs metrics derived from alpha, beta, phylogenetic, taxonomic, and functional diversity, as well as from phenotypes or life strategies derived from genetic potentials. In contrast to addressing operational issues (as noted above), which are effectively addressed by whole population or individual biomarkers, broad improvement and optimisation of function will require enhancement of hydrolysis and acidogenic processes. This will require a discovery-based approach, which will involve integrative research involving the proteome and metabolome. This will utilise, but overcome current limitations of DNA-centric approaches, and likely have broad application outside the specific field of anaerobic digestion.

Enhancing methane production in anaerobic co-digestion of sewage sludge and food waste by regulating organic loading rate

This study presented mechanistic insights into the long-term effects of stepwise-increasing organic loading rates (OLRs) on anaerobic co-digestion (AcoD) of sewage sludge and food waste. The maximum methane (CH₄) yield of 500.0 ± 10.5 mL CH₄/g VS_fed was achieved at medium OLR of 3.5 g VS/L/d. This excellent performance was associated with the high hydrolysis efficiency (78.4%), three-fold enhancement in the acidogenesis enzyme activity, and 87.0% enhanced methanogen activity. Soluble intermediates (carbohydrates and proteins) were largely degraded (>98.5%), especially tyrosine-like and tryptophan-like aromatic proteins. The particulates were effectively decomposed from macromolecules to micromolecules, and the crystallinity of cellulosic substances decreased by 24.5%. The newly-shaped combined syntrophic acetate oxidation-hydrogenotrophic methanogenesis pathway dominated enhanced CH₄ production. Energy balance analysis based on medium OLR demonstrated the high energy recovery potential in full-scale AcoD. These findings suggest the optimal medium OLR can facilitate the bioconversion of organics to CH₄ through a new metabolic pathway.