Deciphering the succession dynamics of dominant and rare genera in biofilm development process

Comprehensive cultivation of the broiler gut microbiota guides bacterial isolation from chickens

Chicken gut microbiota plays an important role in maintaining their physiological health. However, the cultivability of chicken gut microbiota is not well understood, limiting the exploration of certain key gut bacteria in regulating intestinal health and nutritional metabolism. This study aimed to examine the cultivability of chicken cecal microbiota and to provide guidance for future chicken gut microbiota cultivation. A total of 58 different culture conditions were applied to culture broiler cecal microbiota, and the culture-dependent (CD; pooled colonies form each plate) and culture-independent (CI; broiler cecal contents) samples were collected for 16S rRNA gene sequencing and microbial analysis. The CD methods detected higher microbial richness (3,636 vs 2,331 OTUs) than CI methods, and the recovery rates of bacterial OTUs and genera reached 43.6% and 68.9%, respectively. The genera of Bacteroides (19.9%), Alistipes (11.0%) and Barnesiella (10.7%) were highly abundant detected by CI methods, however, there occupied a small proportion (<1.0%) of total cultured microbiota in CD methods. We then developed reference figures and tables showing optimal cultivation conditions for different gut bacteria taxa. Moreover, 81 different lactic acid bacteria strains covering 5 genera were isolated, and 15 strains had less than 97.0% similarity to known bacteria in the national center for biotechnology information (NCBI) online database. Overall, this study provides preliminary guidance in culturing specific gut microbiota from chickens, which will contribute to future studies to characterize the biological functions of key microbes in chicken nutritional metabolism and health.

Exploring interspecific interaction variability in microbiota: A review

Interspecific interactions are an important component and a strong selective force in microbial communities. Over the past few decades, there has been a growing awareness of the variability in microbial interactions, and various studies are already unraveling the inner working dynamics in microbial communities. This has prompted scientists to develop novel techniques for characterizing the varying interspecific interactions among microbes. Here, we review the precise definitions of pairwise and high-order interactions, summarize the key concepts related to interaction variability, and discuss the strengths and weaknesses of emerging characterization techniques. Specifically, we found that most methods can accurately predict or provide direct information about microbial pairwise interactions. However, some of these methods inevitably mask the underlying high-order interactions in the microbial community. Making reasonable assumptions and choosing a characterization method to explore varying microbial interactions should allow us to better understand and engineer dynamic microbial systems.

Linking differences in microbial network structure with changes in coral larval settlement

Coral cover and recruitment have decreased on reefs worldwide due to climate change-related disturbances. Achieving reliable coral larval settlement under aquaculture conditions is critical for reef restoration programmes; however, this can be challenging due to the lack of reliable and universal larval settlement cues. To investigate the role of microorganisms in coral larval settlement, we undertook a settlement choice experiment with larvae of the coral Acropora tenuis and microbial biofilms grown for different periods on the reef and in aquaria. Biofilm community composition across conditioning types and time was profiled using 16S and 18S rRNA gene sequencing. Co-occurrence networks revealed that strong larval settlement correlated with diverse biofilm communities, with specific nodes in the network facilitating connections between modules comprised of low- vs high-settlement communities. Taxa associated with high-settlement communities were identified as Myxoccales sp., Granulosicoccus sp., Alcanivoraceae sp., unassigned JTB23 sp. (Gammaproteobacteria), and Pseudovibrio denitrificans. Meanwhile, taxa closely related to Reichenbachiella agariperforans, Pleurocapsa sp., Alcanivorax sp., Sneathiella limmimaris, as well as several diatom and brown algae were associated with low settlement. Our results characterise high-settlement biofilm communities and identify transitionary taxa that may develop settlement-inducing biofilms to improve coral larval settlement in aquaculture.

Responses of compositions, functions, and assembly processes of bacterial and microeukaryotic communities to long-range voyages in simulated ballast water

Ballast water is one of the main vectors for the spread of harmful organisms among geologically isolated waters. However, the successional processes of microbial functions and assembly processes in ballast water during the long-term shipping voyage remain unclear. In this study, the compositions, ecological functions, community assembly, and potential environmental drivers of bacteria and microeukaryotes were investigated in simulated ballast water microcosms for 120 days. The results showed that the diversity and compositions of the bacterial and microeukaryotic communities varied significantly in the initial 40 days (T0∼T40 samples) and then gradually converged. The relative abundance of Proteobacteria showed a distinct tendency to decrease (87.90%-41.44%), while that of Ascomycota exhibited an increasing trend (6.35%-62.12%). The functional groups also varied significantly over time and could be related to the variations of the microbial community. The chemoheterotrophy and aerobic chemoheterotrophy functional groups for bacteria decreased from 44.80% to 28.02% and from 43.77% to 25.39%, respectively. Additionally, co-occurrence network analysis showed that the structures of the bacterial community in T60∼T120 samples were more stable than those in T0∼T40 samples. Stochastic processes also significantly affected the community assembly of bacteria and microeukaryotes. pH played the most significant role in driving the structures and assembly processes of the bacterial and microeukaryotic communities. The results of this study could aid in the understanding of variations in the functions and ecological processes of bacterial and microeukaryotic communities in ballast water over time and provide a theoretical basis for its management.

Biological functions of endophytic bacteria in Robinia pseudoacacia 'Hongsen'

Introduction

Endophytes and their host plants have co-evolved for a very long time. This relationship has led to the general recognition of endophytes as a particular class of microbial resources. R. pseudoacacia 'Hongsen' is drought- and barren-resistant species that can be grown in both the north and south of China, efficiently addresses the ecological issues caused by China's 'southern eucalyptus and northern poplar. Up to date, cultured-dependent studies are available for the R. pseudoacacia nitrogen-fixing and other endophytes. Therefore, the present research studied the R. pseudoacacia 'Hongsen,' microbiome in detail by high-throughput sequencing and culture dependant.

Methods

This study examined microbial species and functional diversity in Robinia pseudoacacia 'Hongsen' using culture-dependent (isolation) and culture-independent techniques.

Results

A total of 210 isolates were isolated from R. pseudoacacia 'Hongsen.' These isolates were clustered into 16 groups by the In Situ PCR (IS-PCR) fingerprinting patterns. 16S rRNA gene sequence analysis of the representative strain of each group revealed that these groups belonged to 16 species of 8 genera, demonstrating the diversity of endophytes in R. pseudoacacia 'Hongsen'. 'Bacillus is the most prevalent genus among all the endophytic bacteria. High-throughput sequencing of endophytic bacteria from R. pseudoacacia 'Hongsen' of the plant and the rhizosphere soil bacteria showed that the bacterial populations of soil near the root, leaf, and rhizosphere differed significantly. The microbial abundance decreased in the endophytes as compared to the rhizosphere. We observed a similar community structure of roots and leaves. With and without root nodules, Mesorhizobium sp. was significantly different in R. pseudoacacia 'Hongsen' plant.

Discussion

It was predicted that R. pseudoacacia 'Hongsen' plant endophytic bacteria would play a significant role in the metabolic process, such as carbohydrate metabolism, amino acid metabolism, membrane transport, and energy metabolism.

Response mechanism of meiofaunal communities to multi-type of artificial reef habitats from the perspective of high-throughput sequencing technology

Multiple types of artificial reefs have been widely deployed in the coast of northern Yellow Sea, which can enhance fishery resources, restore coastal habitats and improve the marine environment. Meiofauna plays important ecological roles in marine ecosystem, but the response mechanism of meiofaunal community to different types of artificial reef is still poorly understood. In this study, we characterized the meiofaunal communities of concrete artificial reef habitat (CAR), rocky artificial reef habitat (RAR), ship artificial reef habitat (SAR) and adjacent natural habitat (NH) using 18S rRNA gene high-throughput sequencing technology, and explored the relationship of community-environment. The results showed that the diversity and community structure of meiofauna differed significantly on both spatial and temporal scales. Spatial differences were mainly contributed to the flow field effects and biological effects generated by artificial habitats, while temporal differences were driven by temperature (T) and dissolved oxygen (DO). The dominant taxa of meiofauna included arthropods, annelids, platyhelminths and nematodes. Platyhelminths were mainly positively influenced by artificial habitats but annelids were the opposite. Co-occurrence network analysis revealed that NH was more sensitive to environmental change than artificial habitat, while the performance of CAR and SAR were more stable. These results indicated that meiofauna can respond accordingly to different types of artificial habitats, and could be superimposed over the normal seasonal effects. The current study could provide fundamental data for understanding the response mechanism of meiofaunal community to different types of artificial habitats and a reference for assessments of the impact of artificial reefs on the marine environment.

Microbial community shift on artificial biological reef structures (ABRs) deployed in the South China Sea

Many Artificial Reefs (ARs) have been used worldwide for marine habitat and coral reef restoration. However, the microbial community structure that colonize the ARs and their progressive development have been seldom investigated. In this study, the successive development of the microbial communities on environmentally friendly Artificial Biological Reef structures (ABRs)^R made of special concrete supported with bioactive materials collected from marine algal sources were studied. Three seasons (spring, summer and autumn), three coral reef localities and control models (SCE) without bioactive material and (NCE) made of normal cement were compared. The structure of the microbial pattern exhibited successive shifts from the natural environment to the ABRs supported with bioactive materials (ABAM). Cyanobacteria, Proteobacteria, and Planctomycetota were shown to be the most three dominant phyla. Their relative abundances pointedly increased on ABAM and SCE models compared to the environment. Amplicon Sequence Variant (ASV) Richness and Shannon index were obviously higher on ABAM models and showed significant positive relationship with that of macrobenthos than those on the controls and the natural reef (XR). Our results offer successful establishment of healthy microbial films on the ABR surfaces enhanced the restoration of macrobenthic community in the damaged coral reefs which better understands the ecological role of the ABRs.

Unraveling the ecological mechanisms of bacterial succession in epiphytic biofilms on Vallisneria natans and Hydrilla verticillata during bioremediation of phenanthrene and pyrene polluted wetland

In wetland ecosystem, the microbial succession in epiphytic biofilms of submerged macrophytes remains to be fully elucidated, especially submerged macrophytes used to remediate organic pollutants contaminated sediment. Herein, 16 S rRNA gene sequencing was used to investigate the bacterial dynamics and ecological processes in the biofilms of two typical submerged macrophytes (Vallisneria natans and Hydrilla verticillata) settled in sediment polluted by polycyclic aromatic hydrocarbons (PAHs) at two growth periods. The results presented that the variations of bacterial community in the biofilms were influenced by attached surfaces (explanation ratio: 17.30%), incubation time (32.30%) and environmental factors (39.10%). Bacterial community assembly was mainly driven by dispersal limitation which triggered more positive co-occurrence associations in microbial networks, maintaining ecological stability in the process of bioremediation of PAHs. Additionally, the functional redundancy strength of bacterial community was more affected by attached surface than incubation time. The structural equation model illustrated that community assembly drove β-diversity and explained a part of ecological functions. Environmental factors, community assembly, and β-diversity jointly affected microbial networks. Overall, our study offers new insights into the microbial ecology in biofilms attached on the submerged macrophytes settled in PAH-polluted sediment, providing important information for deeply understanding submerged macrophyte-biofilm complex and promoting sustainable phytoremediation in shallow lacustrine and marshy ecosystems.

Research trends and hotspots of aquatic biofilms in freshwater environment during the last three decades: a critical review and bibliometric analysis

Freshwater periphytic biofilms (FPBs), existing widely in various aquatic environments, have attracted extensive attention for many years. In the present study, a bibliometric analysis based on Web of Science Core Collection (WoSCC) was used to understand the research progress, trends, and hot topics of FPBs qualitatively and quantitatively. The results indicated that publications on FPBs have increased from 1991 to 2020 rapidly, and researchers have focused more on the areas of environmental sciences, microbiology, and marine freshwater biology. The most influential countries were mainly the USA, Spain, France, and Germany. Cooperation network analysis reflected that the USA and its affiliated institutions played crucial roles in the research of FPB cooperation, but the collaboration between core author groups still fell short. Based on the analysis of top 20 high-cited FPB documents over the last 30 years, research hotspots mainly included micro-observation and assembly mechanisms of FPBs; interactions of FPBs and pollutants including heavy metals, antibiotic resistance genes, pathogens, organic pollutants, and nanoparticles; and the role of FPBs for biogeochemical cycling, especially nitrogen cycling. Additionally, future research directions were proposed. Overall, this study provides a comprehensive and systematic overview of FPBs, which is useful for research development and researchers who are interested in this area.

Multispecies biofilms in fermentation: Biofilm formation, microbial interactions, and communication

Food fermentation is driven by microorganisms, which usually coexist as multispecies biofilms. The activities and interactions of functional microorganisms and pathogenic bacteria in biofilms have important implications for the quality and safety of fermented foods. It was verified that the biofilm lifestyle benefited the fitness of microorganisms in harsh environments and intensified the cooperation and competition between biofilm members. This review focuses on multispecies biofilm formation, microbial interactions and communication in biofilms, and the application of multispecies biofilms in food fermentation. Microbial aggregation and adhesion are important steps in the early stage of multispecies biofilm formation. Different biofilm-forming abilities and strategies among microorganisms lead to several types of multispecies biofilm formation. The spatial distribution of multispecies biofilms reflects microbial interactions and biofilm function. Then, we discuss the intrinsic factors and external manifestations of multispecies biofilm system succession. Several typical interspecies cooperation and competition modes and mechanisms of microbial communication were reviewed in this review. The main limitations of the studies included in this review are the relatively small number of studies of biofilms formed by functional microorganisms during fermentation and the lack of direct evidence for the formation process of multispecies biofilms and microbial interactions and communication within biofilms. This review aims to provide the food industry with a sufficient understanding of multispecies biofilms in food fermentation. Practical Application: Meanwhile, it offers a reference value for better controlling and utilizing biofilms during food fermentation process, and the improvement of the yield, quality, and safety of fermented products including Chinese Baijiu, cheeese,kefir, soy sauce, kombucha, and fermented olive.

The structure and assembly mechanisms of plastisphere microbial community in natural marine environment

The microbial colonization profiles on microplastics (MPs) in marine environments have recently sparked global interest. However, many studies have characterized plastisphere microbiomes without considering the ecological processes that underly microbiome assembly. Here, we carried out a three-timepoint exposure experiment at 1-, 4-, and 8-week and investigated the colonization dynamics for polyethylene, polypropylene, polystyrene, polyvinyl chloride, and acrylonitrile-butadiene-styrene MP pellets in natural coastal water. Using high-throughput sequencing of 16S rRNA, we found diversity and evenness were higher (p < 0.05) in the plastisphere communities than those in seawater, and microorganisms colonizing were co-influenced by environmental factors, polymer types, and exposure duration. Functional potential and co-occurrence network analysis revealed that MP exposure enriched the xenobiotic biodegradation potential and reduced the complexity of the MP microbial network. Simultaneously, null-model analyses indicated that stochastic processes contributed a bigger role than deterministic processes in shaping plastisphere microbial community structure with dispersal limitations contributing to a greater extent to microbial succession trajectories. These results implied the plastic surface had a more important role as a raft onto which microbes attach rather than selectively recruiting plastic-specific microbial colonizers. Our work strengthened the understanding of the ecological mechanisms by which microbial community patterns are controlled during colonization by plastic-associated microbes.

Risks, characteristics, and control strategies of disinfection-residual-bacteria (DRB) from the perspective of microbial community structure

The epidemic of COVID-19 has aroused people's particular attention to biosafety. A growing number of disinfection products have been consumed during this period. However, the flaw of disinfection has not received enough attention, especially in water treatment processes. While cutting down the quantity of microorganisms, disinfection processes exert a considerable selection effect on bacteria and thus reshape the microbial community structure to a great extent, causing the problem of disinfection-residual-bacteria (DRB). These systematic and profound changes could lead to the shift in regrowth potential, bio fouling potential, as well as antibiotic resistance level and might cause a series of potential risks. In this review, we collected and summarized the data from the literature in recent 10 years about the microbial community structure shifting of natural water or wastewater in full-scale treatment plants caused by disinfection. Based on these data, typical DRB with the most reporting frequency after disinfection by chlorine-containing disinfectants, ozone disinfection, and ultraviolet disinfection were identified and summarized, which were the bacteria with a relative abundance of over 5% in the residual bacteria community and the bacteria with an increasing rate of relative abundance over 100% after disinfection. Furthermore, the phylogenic relationship and potential risks of these typical DRB were also analyzed. Twelve out of fifteen typical DRB genera contain pathogenic strains, and many were reported of great secretion ability. Pseudomonas and Acinetobacter possess multiple disinfection resistance and could be considered as model bacteria in future studies of disinfection. We also discussed the growth, secretion, and antibiotic resistance characteristics of DRB, as well as possible control strategies. The DRB phenomenon is not limited to water treatment but also exists in the air and solid disinfection processes, which need more attention and more profound research, especially in the period of COVID-19.

Comparative Analysis of the Ecological Succession of Microbial Communities on Two Artificial Reef Materials

Concrete and wood are commonly used to manufacture artificial reefs (ARs) worldwide for marine resource enhancement and habitat restoration. Although microbial biofilms play an important role in marine ecosystems, the microbial communities that colonize concrete and wooden ARs and their temporal succession have rarely been studied. In this study, the temporal succession of the microbial communities on concrete and wooden AR blocks and the driving factors were investigated. The composition of the microbial communities underwent successive shifts over time: among the six dominant phyla, the relative abundances of Proteobacteria, Cyanobacteria and Gracilibacteria significantly decreased in wood, as did that of Cyanobacteria in concrete. Operational taxonomic units (OTU) richness and Shannon index were significantly higher in concrete than in wood. Non-metric multidimensional scaling ordination placed the microbial communities in two distinct clusters corresponding to the two substrate materials. The macrobenthic compositions of concrete and wood were broadly similar and shifted over time, especially in the first five weeks. The Shannon index of the microbial communities in concrete and wood increased significantly with the organism coverage. The results provide fundamental data on microbial community succession during the initial deployment of ARs and contribute to understanding the ecological effects of ARs.