Removal of malodorant skatole by two enriched microbial consortia: Performance, dynamic, function prediction and bacteria isolation

Spartina alterniflora Ecosystem Stability: Insights Into the Interplay Between Soil Bacteria and Their Functional Traits

The relationship between soil microbiome stability and diversity remains a topic of debate. Our study aims to investigate the relationship between soil microbiome stability and diversity in different wetland types invaded by Spartina alterniflora and to reveal the mechanisms driving functional influences on this relationship during the later-stage development of the S. alterniflora invasion system. To investigated the structure, diversity, and functional traits of soil bacteria associated with S. alterniflora and their impact on bacteriome stability we conducted 16S rRNA sequencing of soils from two types of wetlands dominated by the invasive plant S. alterniflora at different growth stages, situated in temperate (salt marsh wetland) and subtropical (mangrove wetland) regions, and assessed bacteriome stability and its driving factors. Subsequently, we analyzed environmental and bacterial changes between the two sites and constructed co-occurrence networks among taxonomic groups and functional traits. The differences in the late-stage development of the two S. alterniflora-invaded wetland systems suggest that bacterial communities with higher diversity tend to exhibit greater stability. Keystone genera play both direct and indirect roles in regulating bacteriome stability, and all belong to dominant phyla. Furthermore, biological factors significantly outweigh nonbiological factors in driving stability. In contrast, core functions (broad functions) and specialized functions such as "nitrogen metabolism" and "sulfur metabolism" decrease bacteriome stability. Their enhancement of these metabolic processes correlates with reduced community stability, which is the key to the differences observed in the two invaded systems. This study advances our understanding of the relationship between soil microbial diversity and ecosystem stability, highlighting the importance of keystone taxa and functional traits for soil microbiome stability. It enhances our ability to predict microbial community transitions. It enhances a scientific basis for the management of S. alterniflora invasion.

Advances in microbial degradation of skatole: A review

In recent years, foul odors have led to widespread public complaints and have become a prominent issue in the field of environmental protection. Skatole, as one of the important components of foul odors, is a decomposition product of tryptophan in the intestines of animals and is mainly found in animal feces. Skatole not only has significant pulmonary toxicity to animals but also poses potential carcinogenic risks to humans. The biological method of removing skatole has the notable advantages of being cost-effective, efficient, and environmentally friendly. However, current research on the microbial degradation of skatole is still insufficient, the metabolic pathways for microbial degradation of skatole are not yet fully elucidated, and there is a lack of research on the functional genes involved in degradation. This review outlines skatole's production and distribution in solid, liquid, and gas media, identifies microorganisms capable of skatole degradation, and examines the microbial degradation mechanisms and influencing factors. Additionally, we summarize the hydroxyindole oxidative ring-opening pathway for skatole degradation in anaerobic conditions and multiple aerobic pathways, including oxidative ring-opening and ring-cleaving. Catechol 1,2-dioxygenase is proposed as a key enzyme in the downstream metabolism of microbial skatole degradation, offering guidance for future research.

Microbiome analysis in Asia's largest watershed reveals inconsistent biogeographic pattern and microbial assembly mechanisms in river and lake systems

Microorganisms are critical to the stability of aquatic environments, and understanding the ecological mechanisms of microbial community is essential. However, the distinctions and linkages across biogeographic patterns, ecological processes, and formation mechanisms of microbes in rivers and lakes remain unknown. Accordingly, microbiome-centric analysis was conducted in rivers and lakes in the Yangtze River watershed. Results revealed significant differences in the structure and diversity of microbial communities between rivers and lakes, with rivers showing higher diversity. Lakes exhibited lower community stability, despite higher species interactions. Although deterministic processes dominated microbial community assembly both in rivers and lakes, higher stochastic processes of rare and abundant taxa exhibited in rivers. Spatial factors influenced river microbial community, while environmental factors drove differences in the lake bacterial community. This study deepened the understanding of microbial biogeography and formation mechanisms in large watershed rivers and lakes, highlighting distinct community aggregation patterns between river and lake microorganisms.

Unraveling the skatole biodegradation process in an enrichment consortium using integrated omics and culture-dependent strategies

3-Methylindole (skatole) is regarded as one of the most offensive compounds in odor emission. Biodegradation is feasible for skatole removal but the functional species and genes responsible for skatole degradation remain enigmatic. In this study, an efficient aerobic skatole-degrading consortium was obtained. Rhodococcus and Pseudomonas were identified as the two major and active populations by integrated metagenomic and metatranscriptomic analyses. Bioinformatic analyses indicated that the skatole downstream degradation was mainly via the catechol pathway, and upstream degradation was likely catalyzed by the aromatic ring-hydroxylating oxygenase and flavin monooxygenase. Genome binning and gene analyses indicated that Pseudomonas, Pseudoclavibacter, and Raineyella should cooperate with Rhodococcus for the skatole degradation process. Moreover, a pure strain Rhodococcus sp. DMU1 was successfully obtained which could utilize skatole as the sole carbon source. Complete genome sequencing showed that strain DMU1 was the predominant population in the consortium. Further crude enzyme and RT-qPCR assays indicated that strain DMU1 degraded skatole through the catechol ortho-cleavage pathway. Collectively, our results suggested that synergistic degradation of skatole in the consortium should be performed by diverse bacteria with Rhodococcus as the primary degrader, and the degradation mainly proceeded via the catechol pathway.

Spatiotemporal variations, assembly processes, and co-occurrence patterns of particle-attached and free-living bacteria in a large drinking water reservoir in China

Particle-attached (PA) and free-living (FL) bacterial communities are sensitive to pollutant concentrations and play an essential role in biogeochemical processes and water quality maintenance in aquatic ecosystems. However, the spatiotemporal variations, assembly processes, co-occurrence patterns, and environmental interactions of PA and FL bacteria in drinking water reservoirs remain as yet unexplored. To bridge this gap, we collected samples from 10 sites across four seasons in Lake Tianmu, a large drinking water reservoir in China. Analysis of 16S rRNA gene libraries demonstrated spatiotemporal variations in bacterial diversity and identified differences in bacterial community composition (BCC) between PA and FL lifestyles. Capacity for nitrogen respiration, nitrogen fixation, and nitrate denitrification was enriched in the PA lifestyle, while photosynthesis, methylotrophy, and methanol oxidation were enriched in the FL lifestyle. Deterministic processes, including interspecies interactions and environmental filtration, dominated the assembly of both PA and FL bacterial communities. The influence of environmental filtration on the FL community was stronger than that on the PA community, indicating that bacteria in the FL lifestyle were more sensitive to environmental variation. Co-occurrence patterns and keystone taxa differed between PA and FL lifestyles. The ecological functions of keystone taxa in the PA lifestyle were associated with the supply and recycling of nutrients, while those in FL were associated with the degradation of complex pollutants. PA communities were more stable than FL communities in the face of changing environmental conditions. Nutrients (e.g., TDN and NO₃ ^-) and abiotic and biotic factors (e.g., WT and Chl-a) exerted positive and negative effects, respectively, on the co-occurrence networks of both lifestyles. These results improve our understanding of assembly processes, co-occurrence patterns, and environmental interactions within PA and FL communities in a drinking water reservoir.

Water microecology is affected by seasons but not sediments: A spatiotemporal dynamics survey of bacterial community composition in Lake Changshou-The largest artificial lake in southwest China

This study aimed to evaluate the correlation between microecology of sediments and water as well as their spatial-temporal variations in Changshou Lake. The results demonstrated that microecology in the lake exhibits spatiotemporal heterogeneity, and microbial diversity of sediments was significantly higher than that of water body. Further, it was found that there was statistically insignificant positive correlation between microecology of sediments and that of water body. PCoA and community structure analysis revealed that the predominant phyla which exhibited significant spatial differences in sediments were Proteobacteria, Actinobacteria and Planctomycetes. While, the distribution of dominant bacteria Actinobacteria and Verrucomicrobia in water body showed significant seasonal differences. Microbial networks analysis indicated that there was a cooperative symbiotic relationship between lake microbial communities. Notably, the same bacterial genus had no significant positive correlation in sediment and water, which suggested that bacteria transport between sediment-water interface does not influence the microecological functions of lake water.

pH mediated assemblage of carbon, nitrogen, and sulfur related microbial communities in petroleum reservoirs

Microorganisms are the core drivers of biogeochemistry processes in petroleum reservoirs and have been widely used to enhance petroleum recovery. However, systematic information about the microbial communities related to the C-N-S cycle in petroleum reservoirs under different pH conditions remains poorly understood. In this study, 16S rRNA gene data from 133 petroleum samples were collected, and 756 C-N-S related genera were detected. The Chao1 richness and Shannon diversity indices for the C-N-S-related microbial communities showed significant differences among different pH conditions and at the lowest levels in acidic conditions with pH values of 4.5-6.5. In addition, pH was the most important factor influencing the C-N-S related microbial communities and contributed to 17.95% of the variation in the methanogenesis community. A total of 55 functional genera were influenced by pH, which accounted for 42.08% of the C-N-S related genera. Among them, the genera Pseudomonas and Arcobacter were the highest and were concentrated in acidic conditions with pH values of 4.5-6.5. In parallel, 56 predicted C-N-S related genes were examined, and pH affected 16 of these genes, including putative chitinase, mcrA, mtrB, cysH, narGHIVYZ, nirK, nirB, nifA, sat, aprAB, and dsrAB. Furthermore, the co-occurrence networks of the C-N-S related microbial communities distinctly varied among the different pH conditions. The acidic environment exhibited the lowest complex network with the lowest keystone taxa number, and Escherichia-Shigella was the only keystone group that existed in all three networks. In summary, this study strengthened our knowledge regarding the C-N-S related microbial communities in petroleum reservoirs under different pH conditions, which is of great significance for understanding the microbial ecology and geochemical cycle of petroleum reservoirs.

Keystone Microorganisms Regulate the Methanogenic Potential in Coals with Different Coal Ranks

Microorganisms are the core drivers of coal biogeochemistry and are closely related to the formation of coalbed methane. However, it remains poorly understood about the network relationship and stability of microbial communities in coals with different ranks. In this study, a high-throughput sequencing data set was analyzed to understand the microbial co-occurrence network in coals with different ranks including anthracite, medium-volatile bituminous, and high-volatile bituminous. The results showed similar topological properties for the microbial networks among coals with different ranks, but a great difference was found in the microbial composition in different large modules among coals with different ranks, and these three networks had three, four, and four large modules with seven, nine, and nine phyla, respectively. Among these networks, a total of 46 keystone taxa were identified in large modules, and these keystone taxa were different in coals with different ranks. Bacteria dominated the keystone taxa in the microbial network, and these bacterial keystone taxa mainly belonged to phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Besides, the removal of the key microbial data could reduce the community stability of microbial communities in bituminous coals. A partial least-squares path model further showed that these bacterial keystone taxa indirectly affected methanogenic potential by maintaining the microbial community stability and bacterial diversity. In summary, these results showed that keystone taxa played an important role in determining the community diversity, maintaining the microbial community stability, and controlling the methanogenic potential, which is of great significance for understanding the microbial ecology and the geochemical cycle of coal seams.

Extracellular proteins of Desulfovibrio vulgaris as adsorbents and redox shuttles promote biomineralization of antimony

Biomineralization is the key process governing the biogeochemical cycling of multivalent metals in the environment. Although some sulfate-reducing bacteria (SRB) are recently recognized to respire metal ions, the role of their extracellular proteins in the immobilization and redox transformation of antimony (Sb) remains elusive. Here, a model strain Desulfovibrio vulgaris Hildenborough (DvH) was used to study microbial extracellular proteins of functions and possible mechanisms in Sb(V) biomineralization. We found that the functional groups (N-H, CO, O-CO, NH₂-R and RCOH/RCNH₂) of extracellular proteins could adsorb and fix Sb(V) through electrostatic attraction and chelation. DvH could rapidly reduce Sb(V) adsorbed on the cell surface and form amorphous nanometer-sized stibnite and/or antimony trioxide, respectively with sulfur and oxygen. Proteomic analysis indicated that some extracellular proteins involved in electron transfer increased significantly (p < 0.05) at 1.8 mM Sb(V). The upregulated flavoproteins could serve as a redox shuttle to transfer electrons from c-type cytochrome networks to reduce Sb(V). Also, the upregulated extracellular proteins involved in sulfur reduction, amino acid transport and protein synthesis processes, and the downregulated flagellar proteins would contribute to a better adaption under 1.8 mM Sb(V). This study advances our understanding of how microbial extracellular proteins promote Sb biomineralization in DvH.

Involvement of the metabolically active bacteria in the organic matter degradation during olive mill waste composting

RNA-based high-throughput sequencing is a valuable tool in the discernment of the implication of metabolically active bacteria during composting. In this study, "alperujo" composting was used as microbial model for the elucidation of structure-function relationships with physicochemical transformation of the organic matter. DNA and RNA, subsequently retrotranscribed into cDNA, were isolated at the mesophilic, thermophilic and maturation phases. 16S rRNA gene was amplified by quantitative PCR (qPCR) and Illumina MiSeq platform to assess bacterial abundance and diversity, respectively. The results showed that the abundance of active bacteria assessed by qPCR was maximum at thermophilic phase, which confirm it as the most active stage of the process. Concerning diversity, Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were the main phyla presented in composts. Concomitantly, three different behaviours were observed for bacterial dynamics: some genera decreased during the whole process meanwhile others proliferated only at thermophilic or maturation phase. Statistical correlation between physicochemical transformations of the organic matter and bacterial diversity revealed bacterial specialisation. This result indicated that specific groups of bacteria were only involved in the organic matter degradation during bio-oxidative phase or humification at maturation. Metabolic functions predictions confirmed that active bacteria were mainly involved in carbon (C) and nitrogen (N) cycles transformations, and pathogen reduction.

Bacterial and fungal community compositions and structures of a skatole-degrading culture enriched from pig slurry

In this study, the aerobic activated sludge for skatole removal was enriched from pig slurry in three parallel sequencing batch reactors. The sludge system exhibited a satisfactory performance for skatole removal during the 40 days operation. High-throughput sequencing results showed that the α-diversity remained unchanged before and after the operation process. However, the structures of bacterial and fungal communities notably shifted. Particularly, Arthrobacter increased to be the major bacterial genus from 2.15 ± 0.76% (day 0) to 23.80 ± 24.36% (day 40), and Fusicolla became the major fungal genus from 1.20 ± 0.48% (day 0) to 37.17 ± 7.47% (day 40). These results indicated that Arthrobacter and Fusicolla might participate in skatole removal in sludge systems, though both genera were not reported to be able to degrade skatole. This is the first study describing skatole-degrading bacterial and fungal communities in the enrichment from pig slurry to the best of our knowledge, providing important guidance for skatole control and bioremediation.