Complex Microbial Communities Research Articles

The metabolic burden associated with plasmid acquisition: An assessment of the unrecognized benefits to host cells.

Bacterial conjugation, wherein DNA is transferred between cells through direct contact, is highly prevalent in complex microbial communities and is responsible for spreading myriad genes related to human and environmental health. Despite their importance, much remains unknown regarding the mechanisms driving the spread and persistence of these plasmids in situ. Studies have demonstrated that transferring, acquiring, and maintaining a plasmid imposes a significant metabolic burden on the host. Simultaneously, emerging evidence suggests that the presence of a conjugative plasmid can also provide both obvious and unexpected benefits to their host and local community. Combined, this highlights a continuous cost-benefit tradeoff at the population level, likely contributing to overall plasmid abundance and long-term persistence. Yet, while the metabolic burdens of plasmid conjugation, and their causes, are widely studied, their attendant potential advantages are less clear. Here, we summarize current perspectives on conjugative plasmids' metabolic burden and then highlight the lesser-appreciated yet critical benefits that plasmid-mediated metabolic burdens may provide. We argue that this largely unexplored tradeoff is critical to both a fundamental theory of microbial populations and engineering applications and therefore warrants further detailed study.

Genome Assembly of the Nematode Rhabditoides Inermis From a Complex Microbial Community.

Free-living nematodes such as Caenorhabditis elegans and Pristionchus pacificus are powerful model systems for linking specific traits to their underlying genetic basis. To trace the evolutionary history of specific traits or genes, a robust phylogenomic framework is indispensable. In the context of the nematode family Diplogastridae to which P. pacificus belongs, the identity of a sister group has long been debated. In this work, we generated a pseudochromosome level genome assembly of the nematode Rhabditoides inermis, which has previously been proposed as the sister taxon. The genome was assembled from a complex microbial community that is stably associated with R. inermis isolates and that consists of multiple bacteria and a fungus, which we identified as a strain of Vanrija albida. The R. inermis genome spans 173.5Mb that are largely assembled into five pseudochromosomes. This chromosomal configuration likely arose from two recent fusions of different Nigon elements. Phylogenomic analysis did not support a sister group relationship between R. inermis and diplogastrids, but rather supports a sister group relationship between the monophyletic Diplogastridae and a group of genera of Rhabditidae including C. elegans and R. inermis. Thus, our work addresses for the first time the long lasting question about the sister group to diplogastrids at the phylogenomic level and provides with the genomes of R. inermis and the associated fungus V. albida valuable resources for future genomic comparisons.

Comparative genomic analysis and characterization of novel high-quality draft genomes from the coal metagenome.

Coal, a sedimentary rock harbours a complex microbial community that plays a significant role in its formation and characteristics. However, coal metagenome sequencing and studies were less, limiting our understanding of this complex ecosystem. This study aimed to reconstruct high-quality metagenome-assembled genomes (MAGs) from the coal sample collected in the Neyveli mine to explore the unrevealed diversity of the coal microbiome. Using Illumina sequencing, we obtained high-quality raw reads in FASTQ format. Subsequently, de novo assembly and binning with metaWRAP software facilitated the reconstruction of coal MAGs. Quality assessment using CheckM identified 10 High-Quality MAGs (HQ MAGs), 7 medium-quality MAGs (MQ MAGs), and 6 low-quality MAGs (LQ MAGs). Further analysis using GTDB-Tk revealed four HQ MAGs as known species like Dermacoccus abyssi, Sphingomonas aquatilis, Acinetobacter baumannii, and Burkholderia cenocepacia. The remaining six HQ MAGs were classified as Comamonas, Arthrobacter, Noviherbaspirillum, Acidovorax, Oxalicibacterium, and Bordetella and designated as novel genomes by the validation of digital DNA-DNA hybridization (dDDH). Phylogenetic analysis and further pangenome analysis across the phylogenetic groups revealed a similar pattern with a high proportion of cloud genes. We further analysed the functional potential of these MAGs and closely related genomes using COG. The comparative functional genomics revealed that novel genomes are highly versatile, potentially reflecting adaptations to the coal environment. BlastKOALA was used to conduct a detailed analysis of the metabolic pathways associated with the MAGs. This study highlights the comparative genomic analysis of novel coal genomes with their closely related genomes to understand the evolutionary relationships and functional properties.

Experimental Study on the Removal of Pollutants from Domestic Wastewater in a Strongly Constructed Wetland with an Applied Electric Magnetic Field

The addition of physical field enhancement measures to improve the purification effect of vertical flow artificial wetlands has gradually become popular. In this study, a vertical flow artificial wetland system reinforced by electric and magnetic fields was constructed. These fields were first optimized using finite element 3D simulation software to obtain the optimal electric and magnetic field parameters. Then, the pollutant removal effects and changes in microbial community structure were comparatively analyzed. The optimal electromagnetic field parameters (applied voltage of 15 V and applied magnetic field of 20 mT) resulted in significantly enhanced removal rates of chemical oxygen demand (COD), nitrate nitrogen (NH4+-N), total phosphorus (TP), and orthophosphorus (PO43−-P) in wastewater, with rates of 74.47%, 45.44%, 89.85%, and 90.04%, respectively. These rates were notably higher than those observed in the vertical flow artificial wetland system. The microbial community structure analysis revealed that the vertical flow constructed wetland with enhanced electric and magnetic fields exhibited (EM-VFCW) a more diverse and complex microbial community structure. Notably, the abundance of bacteria capable of removing NH4+-N and COD, including Aspergillus, Fusarium, and Actinobacteria, was significantly elevated.

The gut microbiota modulates airway inflammation in allergic asthma through the gut-lung axis related immune modulation: A review.

The human gut microbiota is a vast and complex microbial community. According to statistics, the number of bacteria residing in the human intestinal tract is approximately 10 times that of total human cells, with over 1,000 different species. The interaction between the gut microbiota and various organ tissues plays a crucial role in the pathogenesis of local and systemic diseases, exerting a significant influence on disease progression. The relationship between the gut microbiota and intestinal diseases, along with its connection to the pulmonary immune environment and the development of lung diseases, is commonly referred to as the "gut-lung axis." The incidence of bronchial asthma is rising globally. With ongoing research on gut microbiota, it is widely believed that intestinal microorganisms and their metabolic products directly or indirectly participate in the occurrence and development of asthma. Based on the gut-lung axis, this review examines recent research suggesting that the intestinal microbiota can influence the occurrence and progression of allergic asthma through the modulation of cytokine immune balance and mucosal integrity. Though the precise immune pathways or microbial species influencing asthma through the gut-lung axis are still under exploration, summarizing the immune modulation through the gut-lung axis in allergic asthma may provide insights for the clinical management of the condition.

Metagenomic discovery of microbial eukaryotes in stool microbiomes.

Host-associated microbiota form complex microbial communities that are increasingly associated with host behavior and disease. While these microbes include bacterial, archaeal, viral, and eukaryotic constituents, most studies have focused on bacteria due to their dominance in the human host and available tools for investigation. Accumulating evidence suggests microbial eukaryotes in the microbiome play pivotal roles in host health, but our understandings of these interactions are limited to a few readily identifiable taxa because of technical limitations in unbiased eukaryote exploration. Here, we combined cell sorting, optimized eukaryotic cell lysis, and shotgun sequencing to accelerate metagenomic discovery and analysis of host-associated microbial eukaryotes. Using synthetic communities with a 1% microbial eukaryote representation, the eukaryote-optimized cell lysis and DNA recovery method alone yielded a 38-fold increase in eukaryotic DNA. Automated sorting of eukaryotic cells from stool samples of healthy adults increased the number of microbial eukaryote reads in metagenomic pools by up to 28-fold compared to commercial kits. Read frequencies for identified fungi increased by 10,000× on average compared to the Human Microbiome Project and allowed for the identification of novel taxa, de novo assembly of contigs from previously unknown microbial eukaryotes, and gene prediction from recovered genomic segments. These advances pave the way for the unbiased inclusion of microbial eukaryotes in deciphering determinants of health and disease in the host-associated microbiome.IMPORTANCEMicrobial eukaryotes are common constituents of the human gut where they can contribute to local ecology and host health, but they are often overlooked in microbiome studies. The lack of attention is due to current technical limitations that are heavily biased or poorly recovered DNA from microbial eukaryotes. We developed a method to increase the representation of these eukaryotes in metagenomic sequencing of microbiome samples that allows to improve their detection compared to prior methods and allows for the identification of new species. Application of the technique to gut microbiome samples improved detection of fungi, protists, and helminths. New eukaryotic taxa and their encoded genes could be identified by sequencing a small number of samples. This approach can improve the inclusion of eukaryotes into microbiome research.

Improving viral annotation with artificial intelligence.

Viruses of bacteria, "phages," are fundamental, poorly understood components of microbial community structure and function. Additionally, their dependence on hosts for replication positions phages as unique sensors of ecosystem features and environmental pressures. High-throughput sequencing approaches have begun to give us access to the diversity and range of phage populations in complex microbial community samples, and metagenomics is currently the primary tool with which we study phage populations. The study of phages by metagenomic sequencing, however, is fundamentally limited by viral diversity, which results in the vast majority of viral genomes and metagenome-annotated genomes lacking annotation. To harness bacteriophages for applications in human and environmental health and disease, we need new methods to organize and annotate viral sequence diversity. We recently demonstrated that methods that leverage self-supervised representation learning can supplement statistical sequence representations for remote viral protein homology detection in the ocean virome and propose that consideration of the functional content of viral sequences allows for the identification of similarity in otherwise sequence-diverse viruses and viral-like elements for biological discovery. In this review, we describe the potential and pitfalls of large language models for viral annotation. We describe the need for new approaches to annotate viral sequences in metagenomes, the fundamentals of what protein language models are and how one can use them for sequence annotation, the strengths and weaknesses of these models, and future directions toward developing better models for viral annotation more broadly.

Rare bacterial taxa drive the ecosystem multifunctionality in lake water-level-fluctuating zone during seasonal water level fluctuations

Complex microbial community plays a crucial role in driving soil ecosystem multifunctionality. Water-level-fluctuating zone (WLFZ) of lakes serves as vital transitional areas between land and water, exhibiting crucial ecological functions. However, the relationship between soil moisture-sensitive bacterial communities and ecosystem multifunctionality remains poorly understood. In this study, we conducted a two-year seasonal field survey in the WLFZ of one large flooding lake. By using amplicon sequencing, we explored the changing characteristics of soil bacterial communities during water level fluctuations and their driving role in ecosystem multifunctionality. A simultaneous decrease in soil bacterial diversity and ecosystem multifunctionality was observed as the soil transitioned from drought to flooding states. Soil bacterial diversity was positively correlated with ecosystem multifunctionality, and rare bacterial sub-communities showed a higher correlation with multifunctionality than the overall bacterial community. Random forest regression analysis demonstrated that rare bacterial sub-communities were the optimal predictor variable for ecosystem multifunctionality in the WLFZ. Additionally, Actinobacteriota and Methylomirabilota held significance in predicting multifunctionality under drought and flooding states, respectively. This study highlighted the predominant role of soil rare bacterial sub-communities in driving ecosystem functionality in the WLFZ.

Metagenomic Analysis: Alterations of Soil Microbial Community and Function due to the Disturbance of Collecting Cordyceps sinensis

Soil microorganisms are critical to the occurrence of Cordyceps sinensis (Chinese Cordyceps), a medicinal fungi used in Traditional Chinese Medicine. The over-collection of Chinese Cordyceps has caused vegetation degradation and impacted the sustainable occurrence of Cordyceps. The effects of Chinese Cordyceps collection on soil microorganisms have not been reported. Metagenomic analysis was performed on the soil of collecting and non-collecting areas of production and non-production areas, respectively. C. sinensis collection showed no alteration in alpha-diversity but significantly affected beta-diversity and the community composition of soil microorganisms. In Cordyceps production, Thaumarchaeota and Crenarchaeota were identified as the dominant archaeal phyla. DNA repair, flagellar assembly, propionate metabolism, and sulfur metabolism were affected in archaea, reducing the tolerance of archaea in extreme habitats. Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Nitrospirae were identified as the dominant bacterial phyla. The collection of Chinese Cordyceps enhanced the bacterial biosynthesis of secondary metabolites and suppressed ribosome and carbon metabolism pathways in bacteria. A more complex microbial community relationship network in the Chinese Cordyceps production area was found. The changes in the microbial community structure were closely related to C, N, P and enzyme activities. This study clarified soil microbial community composition and function in the Cordyceps production area and established that collection clearly affects the microbial community function by altering microbial community structure. Therefore, it would be important to balance the relationship between cordyceps production and microbiology.

Perspectives on the future of ecology, evolution, and biodiversity from the Council on Microbial Sciences of the American Society for Microbiology.

The field of microbial ecology, evolution, and biodiversity (EEB) is at the leading edge of understanding how microbes shape our biosphere and influence the well-being of humankind and Earth. To that end, EEB is developing new transdisciplinary tools to analyze these ecologically critical, complex microbial communities. The American Society for Microbiology's Council on Microbial Sciences hosted a virtual retreat in 2023 to discuss the trajectory of EEB both within the Society and microbiology writ large. The retreat emphasized the interconnectedness of microbes and their outsized global influence on environmental and host health. The maximal potential impact of EEB will not be achieved without contributions from disparate fields that unite diverse technologies and data sets. In turn, this level of transdisciplinary efforts requires actively encouraging "broad" research, spanning inclusive global collaborations that incorporate both scientists and the public. Together, the American Society for Microbiology and EEB are poised to lead a paradigm shift that will result in a new era of collaboration, innovation, and societal relevance for microbiology.

Bacteriophage-mediated approaches for biofilm control.

Biofilms are complex microbial communities in which planktonic and dormant bacteria are enveloped in extracellular polymeric substances (EPS) such as exopolysaccharides, proteins, lipids, and DNA. These multicellular structures present resistance to conventional antimicrobial treatments, including antibiotics. The formation of biofilms raises considerable concern in healthcare settings, biofilms can exacerbate infections in patients and compromise the integrity of medical devices employed during treatment. Similarly, certain bacterial species contribute to bulking, foaming, and biofilm development in water environments such as wastewater treatment plants, water reservoirs, and aquaculture facilities. Additionally, food production facilities provide ideal conditions for establishing bacterial biofilms, which can serve as reservoirs for foodborne pathogens. Efforts to combat antibiotic resistance involve exploring various strategies, including bacteriophage therapy. Research has been conducted on the effects of phages and their individual proteins to assess their potential for biofilm removal. However, challenges persist, prompting the examination of refined approaches such as drug-phage combination therapies, phage cocktails, and genetically modified phages for clinical applications. This review aims to highlight the progress regarding bacteriophage-based approaches for biofilm eradication in different settings.

One-Step Soft Agar Enrichment and Isolation of Human Lung Bacteria Inhibiting the Germination of Aspergillus fumigatus Conidia

Fungi of the genus Aspergillus are widespread in the environment, where they produce large quantities of airborne conidia. Inhalation of Aspergillus spp. conidia in immunocompromised individuals can cause a wide spectrum of diseases, ranging from hypersensitivity responses to lethal invasive infections. Upon deposition in the lung epithelial surface, conidia encounter and interact with complex microbial communities that constitute the lung microbiota. The lung microbiota has been suggested to influence the establishment and growth of Aspergillus spp. in the human airways. However, the mechanisms underlying this interaction have not yet been sufficiently investigated. In this study, we aimed to enrich and isolate bacterial strains capable of inhibiting the germination and growth of A. fumigatus conidia from bronchoalveolar lavage fluid (BALF) samples of lung transplant recipients using a novel enrichment method. This method is based on a soft agar overlay plate assay in which bacteria are directly in contact with conidia, allowing inhibition to be readily observed during enrichment. We isolated a total of five clonal bacterial strains with identical genotypic fingerprints, as shown by random amplified polymorphic DNA PCR (RAPD–PCR). All strains were identified as Pseudomonas aeruginosa (strains b1–b5). The strains were able to inhibit the germination and growth of Aspergillus fumigatus in a soft agar confrontation assay, as well as in a germination multiplate assay. Moreover, when compared with ten P. aeruginosa strains isolated from expectoration through standard methods, no significant differences in inhibitory potential were observed. Additionally, we showed inhibition of A. fumigatus growth on Calu-3 cell culture monolayers. However, the isolated P. aeruginosa strains were shown to cause significant damage to the cell monolayers. Overall, although P. aeruginosa is a known opportunistic lung pathogen and antagonist of A. fumigatus, we validated this novel one-step enrichment approach for the isolation of bacterial strains antagonistic to A. fumigatus from BALF samples as a proof-of-concept. This opens up a new venue for the targeted enrichment of antagonistic bacterial strains against specific fungal pathogens.

Sophorolipid: An Effective Biomolecule for Targeting Microbial Biofilms.

Biofilms are microbial aggregates encased in a matrix that is attached to biological or nonbiological surfaces and constitute serious problems in food, medical, and marine industries and can have major negative effects on both health and the economy. Biofilm's complex microbial community provides a resistant environment that is difficult to eradicate and is extremely resilient to antibiotics and sanitizers. There are various conventional techniques for combating biofilms, including, chemical removal, physical or mechanical removal, use of antibiotics and disinfectants to destroy biofilm producing organisms. In contrast to free living planktonic cells, biofilms are very resistant to these methods. Hence, new strategies that differ from traditional approaches are urgently required. Microbial world offers a wide range of effective "green" compounds such as biosurfactants. They outperform synthetic surfactants in terms of biodegradability, superior stabilization, and reduced toxicity concerns. They also have better antiadhesive and anti-biofilm capabilities which can be used to treat biofilm-related problems. Sophorolipids (SLs) are a major type of biosurfactants that have gained immense interest in the healthcare industries because of their antiadhesive and anti-biofilm properties. Sophorolipids may therefore prove to be attractive substances that can be used in biomedical applications as adjuvant to other antibiotics against some infections through growth inhibition and/or biofilm disruption.

Selection for amoxicillin-, doxycycline-, and enrofloxacin-resistant Escherichia coli at concentrations lower than the ECOFF in broiler-derived cecal fermentations.

Antimicrobial resistance (AMR) is an emerging worldwide problem and a health threat for humans and animals. Antimicrobial usage in human and animal medicine or in agriculture results in selection for AMR. The selective concentration of antimicrobial compounds can be lower than the minimum inhibitory concentration and differs between environments, which can be a reason for bacterial resistance. Therefore, knowledge of the minimal selective concentration (MSC), under natural conditions, is essential to understand the selective window of bacteria when exposed to residual antimicrobials. In this study, we estimated the MSCs of three antimicrobials, amoxicillin, doxycycline, and enrofloxacin in a complex microbial community by conducting fermentation assays with cecal material derived from broilers. We examined the phenotypic resistance of Escherichia coli, resistome, and microbiome after 6 and 30 hours of fermenting in the presence of the antimicrobials of interest. The concentrations were estimated to be 10-100 times lower than the epidemiological cut-off values in E. coli for the respective antimicrobials as determined by EUCAST, resulting in an MSC between 0.08 and 0.8 mg/L for amoxicillin, 0.4 and 4 mg/L for doxycycline, and 0.0125 and 0.125 mg/L for enrofloxacin. Additionally, resistome analysis provided an MSC for doxycycline between 0.4 and 4 mg/L, but amoxicillin and enrofloxacin exposure did not induce a significant difference. Our findings indicate at which concentrations there is still selection for antimicrobial-resistant bacteria. This knowledge can be used to manage the risk of the emergence of antimicrobial-resistant bacteria.IMPORTANCEAntimicrobial resistance possibly affects human and animal health, as well as economic prosperity in the future. The rise of antimicrobial-resistant bacteria is a consequence of using antimicrobial compounds in humans and animals selecting for antimicrobial-resistant bacteria. Concentrations reached during treatment are known to be selective for resistant bacteria. However, at which concentrations residues are still selective is important, especially for antimicrobial compounds that remain in the environment at low concentrations. The data in this paper might inform decisions regarding guidelines and regulations for the use of specific antimicrobials. In this study, we are providing these minimal selective concentrations for amoxicillin, doxycycline, and enrofloxacin in complex environments.

Role of TM7 in the Oral Microbiome and its Implications for Periodontal Disease: A Systematic Review

ABSTRACT Periodontal disease, a prevalent oral health condition, involves a complex microbial community. Advanced sequencing technologies have enabled in-depth studies of the oral microbiome, focusing on specific bacterial taxa like TM7. This systematic review analyzes the role of TM7 in the oral microbiome and its implications for periodontal disease. This review underscores TM7’s importance in the oral microbiome and its potential as a target for future research on periodontal disease pathogenesis.

Classifying compounds as prebiotics - scientific perspectives and recommendations.

Microbiomes provide key contributions to health and potentially important therapeutic targets. Conceived nearly 30 years ago, the prebiotic concept posits that targeted modulation of host microbial communities through the provision of selectively utilized growth substrates provides an effective approach to improving health. Although the basic tenets of this concept remain the same, it is timely to address certain challenges pertaining to prebiotics, including establishing that prebiotic-induced microbiota modulation causes the health outcome, determining which members within a complex microbial community directly utilize specific substrates in vivo and when those microbial effects sufficiently satisfy selectivity requirements, and clarification of the scientific principles on which the term 'prebiotic' is predicated to inspire proper use. In this Expert Recommendation, we provide a framework for the classification of compounds as prebiotics. We discuss ecological principles by which substrates modulate microbiomes and methodologies useful for characterizing such changes. We then propose statistical approaches that can be used to establish causal links between selective effects on the microbiome and health effects on the host, which can help address existing challenges. We use this information to provide the minimum criteria needed to classify compounds as prebiotics. Furthermore, communications to consumers and regulatory approaches to prebiotics worldwide are discussed.

The TELCoMB Protocol for High-Sensitivity Detection of ARG-MGE Colocalizations in Complex Microbial Communities.

Understanding the genetic basis of antimicrobial resistance is crucial for developing effective mitigation strategies. One necessary step is to identify the antimicrobial resistance genes (ARGs) within a microbial population, referred to as the resistome, as well as the mobile genetic elements (MGEs) harboring ARGs. Although shotgun metagenomics has been successful in detecting ARGs and MGEs within a microbiome, it is limited by low sensitivity. Enrichment using cRNA biotinylated probes has been applied to address this limitation, enhancing the detection of rare ARGs and MGEs, especially when combined with long-read sequencing. Here, we present the TELCoMB protocol, a Snakemake workflow that elucidates resistome and mobilome composition and diversity and uncovers ARG-MGE colocalizations. The protocol supports both short- and long-read sequencing and does not require enrichment, making it versatile for various genomic data types. TELCoMB generates publication-ready figures and CSV files for comprehensive analysis, improving our understanding of antimicrobial resistance mechanisms and spread. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Installing TELCOMB Locally Alternate Protocol: Installing TELCOMB on a SLURM Cluster Basic Protocol 2: Data Preprocessing Basic Protocol 3: Calculation of Resistome Distribution and Composition Basic Protocol 4: Identification of ARG-MGE Colocalizations.

Mechanism of carbonized humic acid and magnesium aluminum-layered double hydroxide promoting biohydrogen generation

Dark fermentation (DF) is prone to low hydrogen (H2) yield. In this work, magnesium aluminum-layered double hydroxide and carbonized humic acid (MgAl-LDH/CHA) was synthesized by co-precipitation to reveal the mechanism in rising bioH2 generation. The results indicated that MgAl-LDH released Mg and Al ions slowly in DF system, improving the activity of H2-producing microbes (HPM) for more H2. The H2 yield increased from 169.3 mL/g glucose to 244.9 mL/g glucose, which was 44.7 % higher than that for the control yield. MgAl-LDH/CHA increased Proteobacteria content from 30.9 % to 43.7 %, making it form a complex microbial community and participate in DF metabolism with Firmicutes and other microbes together. Besides, MgAl-LDH/CHA could serve as an electron shuttle that likely effectively promotes electron transfer in DF, significantly reduced the energy requirements of HPM, thus raising metabolic activity. It provides direction for the multi-element composite applied in DF system.

Persistent tissue-specific resident microbiota in oysters across a broad geographical range.

Marine animals often harbour complex microbial communities that influence their physiology. However, strong evidence for resident microbiomes in marine bivalves is lacking, despite their contribution to estuarine habitats and coastal economies. We investigated whether marine bivalves harbour stable, resident microorganisms in specific tissues or if their microbiomes primarily consist of transient members reflecting the environmental microbial pool. Conducting a latitudinal study of wild eastern oysters (Crassostrea virginica) along the East Coast of the United States, we aimed to identify resident microorganisms that persist across a wide geographical range. Our results revealed that microbial communities in seawater and sediment samples followed latitudinal diversity patterns driven by geographic location. In contrast, oyster-associated microbiomes were distinct from their surrounding environments and exhibited tissue-specific compositions. Notably, oyster microbiomes showed greater similarity within the same tissue type across different geographic locations than among different tissue types within the same location. This indicates the presence of tissue-specific resident microbes that persist across large geographical ranges. We identified a persistent set of resident microbiome members for each tissue type, with key microbial members consistent across all locations. These findings underscore the oyster host's role in selecting its microbiome and highlight the importance of tissue-specific microbial communities in understanding bivalve-associated microbiomes.

Unique ecology of biofilms and flocs: Bacterial composition, assembly, interaction, and nitrogen metabolism within deteriorated bioreactor inoculated with mature partial nitrification-anammox sludge

This work unraveled discrepant ecological patterns between biofilms and flocs in a deteriorated bioreactor inoculated with mature partial nitrification-anammox (PN/A) sludge. Based on 16S rRNA analysis, a comprehensive evaluation of neutral and null models, along with niche width, delineated that the bacterial community assembly in biofilms and flocs was dominantly driven by the stochastic process, and dispersal limitation critically shaped the community assembly. Co-occurrence network analysis revealed that environmental stress caused decentralized and fragmented bacterial colonies, and anammox bacteria were mainly peripheral in biofilms network and less involved in interspecific interactions. Simultaneous PN/A and partial denitrification-anammox (PD/A) processes were identified, whereas PN and PD process primarily occurred in the biofilms and flocs, respectively, as evidenced by metagenomics. Collectively, these outcomes are expected to deepen the basic understanding of complex microbial community and nitrogen metabolism under environmental disturbance, thereby better characterizing and serving the artificial ecosystems.