Marine microbial community dynamics and their ecological interpretation

Ecological divergence of marine bacteria Alteromonas mediterranea

Alteromonas mediterranea, originally designated as A. macleodii, is a deep-sea ecotype that plays an important ecological role in the ocean. However, a comprehensive understanding of their biogeographic distribution and evolutionary histories remains limited. In this study, our analysis indicated that A. mediterranea members could adapt contrasting marine ecosystems and flourish in nutrient-rich habitats such as feces and coral reefs. No significant correlations between the relative abundance of A. mediterranea members and the environmental variables were identified. Phylogenetic analysis and geographic patterns of A. mediterranea strains suggested that they could be clustered into two clades (clade Ⅰ and clade Ⅱ). In contrast, many distinct genomic traits exist between these clades, such as the complete genes encoding cytochrome o ubiquinol oxidase only involved in clade Ⅱ. Genes were more likely to be lost in the evolutionary history of A. mediterranea relatives. Gene loss might be a major force in all phylogenetic groups driving the distinct clades. Adaptation to different biotopes resulted in the functional differentiation of A. mediterranea members, with the loss of genes encoding carbohydrate-active enzymes. Genes acquired horizontally from unclassified bacteria, and Proteobacteria represented by Gammaproteobacteria played key roles in the functional diversification of A. mediterranea in marine habitats. Given these data, these results are useful for information supplementation of A. mediterranea strains, particularly for making significant advances in understanding marine microbial ecology within different clonal frames using genome-wide recruitments.

Community stability of free-living and particle-attached prokaryotes in coastal waters across four seasons: insights from 9.5 years of weekly sampling

Free-living (FL) and particle-attached (PA) prokaryotes, having distinct ecological niches, play significant roles in marine ecosystems. These communities respond rapidly to environmental changes and exhibit seasonal patterns. However, their temporal stability, crucial for maintaining microbial community structure and function, remains poorly understood. This study assessed community stability, particularly in terms of resistance to environmental perturbations, and inferred regulatory mechanisms using weekly collected samples over 9.5 years from FL and PA communities in coastal water. Short-read amplicon sequencing revealed habitat-specific microbial compositions, with Actinobacteria and Euryarchaeota dominating FL community, while Planctomycetes and Verrucomicrobia prevailed in PA community. Network analysis, constructed based on relative abundance, uncovered seasonal co-occurrence patterns and highlighted keystone taxa, such as Nitrosopumilus in FL and Synechococcus in PA community, as critical for maintaining stability within specific seasons and niches. Seasonal variations in community stability indices suggest that higher network complexity can enhance resistance; however, excessive interactions with greater complexity may also undermine it. Furthermore, it was found that FL community stability was primarily affected by abiotic factors, likely due to direct exposure to environmental changes, whereas PA community stability was more influenced by biotic factors, as their association with particles fosters localized interactions and biological processes. These findings reveal the intricate balance between network complexity and stability and the importance of niche-specific approaches in ecological research. Our results contribute to a deeper understanding of marine microbial niche partitioning and provide insights into ecosystem management and conservation strategies, particularly regarding keystone taxa.

CABO-16S-a Combined Archaea, Bacteria, Organelle 16S rRNA database framework for amplicon analysis of prokaryotes and eukaryotes in environmental samples

Identification of both prokaryotic and eukaryotic microorganisms in environmental samples is currently challenged by the need for additional sequencing to obtain separate 16S and 18S ribosomal RNA (rRNA) amplicons or the constraints imposed by "universal" primers. Organellar 16S rRNA sequences are amplified and sequenced along with prokaryote 16S rRNA and provide an alternative method to identify eukaryotic microorganisms. CABO-16S combines bacterial and archaeal sequences from the SILVA database with 16S rRNA sequences of plastids and other organelles from the PR2 database to enable identification of all 16S rRNA sequences. Comparison of CABO-16S with SILVA 138.2 results in equivalent taxonomic classification of mock communities and increased classification of diverse environmental samples. In particular, identification of phototrophic eukaryotes in shallow seagrass environments, marine waters, and lake waters was increased. The CABO-16S framework allows users to add custom sequences for further classification of underrepresented clades and can be easily updated with future releases of reference databases. Addition of sequences obtained from Sanger sequencing of methane seep sediments and curated sequences of the polyphyletic SEEP-SRB1 clade resulted in differentiation of syntrophic and non-syntrophic SEEP-SRB1 in hydrothermal vent sediments. CABO-16S highlights the benefit of combining and amending existing training sets when studying microorganisms in diverse environments.

Microbial communities and fatty acid markers across acidification and eutrophication extremes in a river influenced by mining activities

Microbial communities in combination with fatty acid and isotopic markers were studied seasonally to assess the effects of acid mine drainage (AMD) and nutrient loads in the Spree river. Negative values of δ15N, the bacterial and detrital markers 18: 1(n-7) and 18:1(n-9), pH values ∼3 and bacteria of the genera Ferrovum, Thiomonas, Acidocella, Acidiphilum, Syderoxydans and Galionella were characteristic of the AMD extreme. Potential iron-oxidizers may produce ferric ions and their precipitates may influence biogeochemical processes, while potential sulfur-oxidizers may contribute to elevated sulphate concentrations and challenge drinking water production in the Spree catchment. In this river, eutrophication was linked with polyunsaturated fatty acids (PUFA) enrichment and not with PUFA depletion as occurs in other freshwater systems. Elevated concentrations and proportions of PUFA as well as higher relative sequence abundance of cyanobacteria were characteristic of the highly eutrophic station, particularly during the phytoplankton bloom. The 18:5(n-3) from flagellates or dinoflagellates may indicate lipid anabolism and trophic upgrading processes. The dominance of the classes Bacteroidia, Gammaproteobacteria and Actinobacteria suggested eutrophic and changing hydrological conditions in the river. The microbial communities were better markers of seasonality than the biogeochemical markers and their combination offers an excellent resolution for the study of the ecology and biogeochemistry of water courses. The expected decreased runoff under climate-driven scenarios may worsen the AMD pollution and eutrophication problems and signify a considerable challenge for water management.

Bacteriophage-driven microbial phenotypic heterogeneity: ecological and biogeochemical importance

Bacteriophages (phages) reprogram host metabolism and generate phenotypic heterogeneity, yet the mechanisms and ecological implications remain poorly understood representing a major knowledge gap in microbial ecology. This review explores how phage infection alters microbial physiology, contributes to single-cell variation, and influences population dynamics. We highlight the potential consequences of phage-driven heterogeneity for microbial community structure and biogeochemical cycling, underscoring the importance of integrating phage-host interactions into ecological and ecosystem models.

Use of Ecological Networks to Reveal Interspecific Fungal Interactions from 150 Years of Foray Records

Fungal forays have been conducted for more than 150 years, providing valuable, but underutilized, sets of records for studies of fungal ecology. Although foray records have been used to study species composition and phenological change, their potential of revealing internal interactions within fungal communities has not been explored. This paper collates foray records conducted in Yorkshire over the past 150 years focusing on 12 autumn-fruiting, generalist ectomycorrhizal fungal species. Using network and co-occurrence analysis, the study has identified and characterized the community characteristics between the species, identifying highly influential species and significant interactions between species. The results demonstrate the potential of foray records in detecting interspecific fungal interactions and highlight their potential to contribute to future research in fungal community ecology.

Environmental Heterogeneity Drives Ecological Differentiation in Vibrio Populations Across Subtropical Marine Habitats

Elucidating how environmental gradients structure bacterial communities remains fundamental to microbial ecology. We investigated Vibrio population dynamics across contrasting subtropical marine environments in Hong Kong over a year period. Using an integrated approach combining cultivation techniques with molecular analyses of Hsp60 and 16S rRNA genes, we characterised the population structure between a coastal site (Clear Water Bay) and an estuarine site (Deep Bay). The estuarine environment consistently harboured higher Vibrio abundances (104-107 copies/mL) compared to coastal waters (102-104 copies/mL), with significantly greater phylogenetic diversity. Multivariate analyses revealed salinity as the primary driver of community differentiation between sites, while temperature governed seasonal succession patterns. Phylogenetic analysis of 1521 Vibrio isolates identified three distinct ecological groups corresponding to specific temperature-salinity niches, with evidence of habitat-specific thermal adaptations among closely related strains. Experimental characterisation of thermal performance curves confirmed physiological differentiation between warm- and cool-temperature adapted strains despite high genetic similarity (> 97% Hsp60 gene sequence identity). Several abundant species detected via amplicon sequencing (including V. navarrensis and V. mimicus) displayed site-specific ecotypes but remained uncultivated, highlighting methodological constraints in community characterisation. Our findings demonstrate how environmental heterogeneity drives fine-scale ecological differentiation in Vibrio populations, providing insights into mechanisms of bacterial adaptation in dynamic marine environments.

Low oxygen in the open ocean: A case study of mild oxygen minimum zone (OMZ) in the Western Pacific

Marine hypoxia, exacerbated by global warming, has led to the expansion of oxygen minimum zone (OMZ) in the ocean. Based on investigations across four sections in the Tropical Western Pacific Ocean, this study examines the characteristics and key controlling factors of OMZ in the region, with a focus on the interactions between organic matter and hypoxia, using particulate organic carbon (POC) as an example. Results indicate that OMZ are located at depths of 550-1380 m, 290-1120 m, 740-1380 m, and 730-1380 m across the four sections, with a dissolved oxygen threshold of 3.2 mg/L. Seawater stratification plays a crucial role in defining OMZ distribution, with OMZ upper boundaries occurring below the halocline and minimum oxygen levels found beneath the thermocline. Ocean circulation facilitates the westward expansion of the intense OMZ from the Eastern Pacific, influencing its extent in the study area. OMZ enhance the transport of POC to the deep sea, with decomposition rates within OMZ significantly lower than in overlying waters, 17.7 %, 3.1 %, 3.7 %, and 13.6 % in sections A, B, C, and D, respectively. These findings provide valuable insights into the fundamental characteristics, drivers, and biogeochemical implications of OMZ in the Western Pacific.

Bacterial community analysis of recreational beach waters reveals human fecal contamination and pathogenicity across varying field conditions

Assessing human fecal contamination of recreational beach waters is a public health challenge owing to multiple sources and environmental conditions affecting indicator, pathogen, and source marker relationships. Human fecal-associated markers, such as HF183, accurately indicate human waste, but reliance on individual markers risks false negative diagnoses, owing to marker source loading variations and attenuation. Bacterial community analysis is a data-dense approach that could improve the accuracy of human waste detection, but relatedness to actual human health hazards under complex coastal water conditions is unproven. Here, two Malibu and one Pacific Palisades, CA recreational beaches differing in urbanization and sewerage were studied over two years across varying seasonal rainfall, and beach berm, conditions. Fecal indicator bacteria (FIB), HF183, and human norovirus concentrations were quantified and related to bacterial community 16S rRNA gene sequences which were further analyzed for putative human pathogens and sewage proportions. All lower watersheds harbored human fecal sources, and surf zone contamination was enhanced by rainfall runoff with berm breaching, which intensified with urbanization. Notably, for sequenced surf zone waters sampled across all weather conditions (n = 36), sequence-based putative pathogen proportions correlated with qPCR HF183 concentrations (w/ and w/o PMA treatment; p = 0.0) and with human norovirus G1concentrations (p = 0.04) which also correlated with HF183 sequence abundance in bacterial communities (p = 0.02). Although human fecal sources appeared to vary seasonally and a range of physical conditions influenced surf zone fecal contamination, human fecal contamination and associated health hazard were reliably evidenced by bacterial community analysis in this study.

Alterations in bacterial structure and function in seawater due to Mytilus coruscus farming: implications for sustainable aquaculture management

Microorganisms are essential for maintaining the ecological balance and supporting the health of aquatic animals in aquaculture environments. This study utilized high-throughput sequencing technology to analyze the diversity, composition, co-occurrence networks, assembly mechanisms, and functional predictions of bacterial communities in seawater from both Mytilus coruscus aquaculture areas (AA) and non-aquaculture areas (NAA) across different seasons. The results indicated that the number of operational taxonomic units (OTUs) in the AA group was higher than the NAA group, while the Simpson index was significantly lower in the bottom water (p < 0.05). Additionally, the β-diversity (Bray-Curtis distance and βMNTD) was significantly reduced in the AA group compared to the NAA group (p < 0.05). M. coruscus farming influenced the relative abundance of certain genera, including Pseudoalteromonas, HIMB11, and Clade Ia, with the AA group exhibiting a greater number of specialist species. Co-occurrence network analysis revealed that the bacterial network in the NAA group had a higher number of nodes, edges, and modularity, whereas the AA group displayed greater closeness centrality and betweenness centrality. Following the removal of 80% of the nodes, the natural connectivity of the surface water in the AA group declined more rapidly than in the NAA group. Homogeneous selection was the primary assembly mechanism of bacterial communities in the AA group, while diffusion limitation was predominant in the NAA group. FAPROTAX functional predictions indicated the higher relative abundance of functions associated with organic matter degradation and nitrogen cycling in the AA group. These findings suggest that M. coruscus farming activities significantly alter the structure and function of bacterial communities in seawater, providing valuable data to support sustainable aquaculture for M. coruscus and optimize fisheries' carbon sink management strategies.

Unveiling Short-Scale Responses: How Pico- and Nanoeukaryotic Plankton Navigate Environmental Variability in a Coastal Upwelling System

For decades, identifying pico- and nanoeukaryotic plankton has been challenging due to their small size, leaving a significant gap in our knowledge of their composition and dynamics in comparison with their larger counterparts. The advent of molecular techniques unlocked new possibilities for exploring this hidden diversity. We applied metabarcoding targeting the V9 region of 18S rDNA to discern the principal taxonomic groups of pico- and nanoeukaryotes in the Ría de Vigo during the upwelling season. Nanoeukaryotes (NE) exhibit greater diversity compared to picoeukaryotes (PE). Specifically, NE were mainly comprised of nano-sized diatoms and dinoflagellates, many of them uncategorized novel species. Within PE, Syndiniales and Marine Stramenopiles (MAST) were the main components identified. We also captured short-term changes in the biomass and composition of PE an NE, with advection emerging as one of the most significant drivers. Most notably was the ocean inflow of unassigned picoeukaryotes into the Ría, likely driven by the negative circulation during downwelling. Moreover, local grazing within the Ría seems to be important enough to alter NE dynamics, but has a minimal effect over PE. Our findings improve the understanding of the small eukaryotic plankton community in coastal upwelling systems, highlighting a significant potential for novel diversity within these environments.

A critical review of microbial profiles in black and odorous waters

Black and odorous waters (BOWs) are a serious environmental problem frequently reported over the past few decades. Microorganisms are identified as implementors of the black and odorous phenomenon, which play a crucial role in the decomposition and transformation of pollutants within the BOWs. However, the information on the role of microorganisms in BOWs remains elusive. BOWs are characterized by high concentrations of organic compounds and limited oxygen inputs, which have facilitated the emergence of distinct microbial species. The algae, hydrolytic and fermentative bacterium, sulfate-reducing bacteria, Fe-reducing bacteria and other microorganisms play an important role in the process of blackening and odorization of waters. Studying these specific microbial taxonomies provides valuable insights into their adaptations and contributions to the overall functioning of BOWs. This study comprehensively reviews 1) the microbial community structure, assembly and succession in BOWs; 2) the key microbial profiles involved in BOWs formation; 3) the interspecies interactions process in the BOWs, which are the issues easily overlooked but deserve further research and development.

Light-Mediated Population Dynamics of Picocyanobacteria Shaping the Diurnal Patterns of Microbial Communities in an Atoll Lagoon

The diurnal cycle of light significantly impacts microbes, making diurnal investigations crucial for understanding microbial communities. Zhubi Reef is known to harbor exceptionally rich biodiversity, with both zooplankton and seawater properties demonstrating diurnal patterns. However, microbial community structures and their potential diurnal dynamics remain largely unexplored. This study is the first to utilize flow cytometry and high-throughput sequencing to investigate prokaryotic and microeukaryotic communities in the Zhubi lagoon, focusing on diurnal variations under different light intensities. The picophytoplankton cell abundance and the microbial community structures both exhibit clear diurnal variations. Light is identified as the primary driver of diurnal variations in the picophytoplankton cell abundance. The diurnal variation in microbial community diversity is driven by changes in the cell abundance of two dominant picocyanobacterial groups. Our findings reveal the diurnal variation in microbial community structures is mediated by the light-driven fluctuation of dominant cyanobacterial populations, and the diurnal variation patterns of specific populations may vary with habitats and sampling timepoints. This research provides valuable insights into the microbial community structure within the Zhubi lagoon.

Last Decade Insights in Exploiting Marine Microorganisms as Sources of New Bioactive Natural Products

Marine microorganisms have emerged as prolific sources of bioactive natural products, offering a large chemical diversity and a broad spectrum of biological activities. Over the past decade, significant progress has been made in discovering and characterizing these compounds, pushed by technological innovations in genomics, metabolomics, and bioinformatics. Furthermore, innovative isolation and cultivation approaches have improved the isolation of rare and difficult-to-culture marine microbes, leading to the identification of novel secondary metabolites. Advances in synthetic biology and metabolic engineering have further optimized natural product yields and the generation of novel compounds with improved bioactive properties. This review highlights key developments in the exploitation of marine bacteria, fungi, and microalgae for the discovery of novel natural products with potential applications in diverse fields, underscoring the immense potential of marine microorganisms in the growing Blue Economy sector.

Cross-validation for training and testing co-occurrence network inference algorithms

BACKGROUND

Microorganisms are found in almost every environment, including soil, water, air and inside other organisms, such as animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as decomposition, fermentation and nutrient cycling. Much research has been conducted on the study of microbial communities in various environments and how their interactions and relationships can provide insight into various diseases. Co-occurrence network inference algorithms help us understand the complex associations of micro-organisms, especially bacteria. Existing network inference algorithms employ techniques such as correlation, regularized linear regression, and conditional dependence, which have different hyper-parameters that determine the sparsity of the network. These complex microbial communities form intricate ecological networks that are fundamental to ecosystem functioning and host health. Understanding these networks is crucial for developing targeted interventions in both environmental and clinical settings. The emergence of high-throughput sequencing technologies has generated unprecedented amounts of microbiome data, necessitating robust computational methods for network inference and validation.

RESULTS

Previous methods for evaluating the quality of the inferred network include using external data, and network consistency across sub-samples, both of which have several drawbacks that limit their applicability in real microbiome composition data sets. We propose a novel cross-validation method to evaluate co-occurrence network inference algorithms, and new methods for applying existing algorithms to predict on test data. Our method demonstrates superior performance in handling compositional data and addressing the challenges of high dimensionality and sparsity inherent in real microbiome datasets. The proposed framework also provides robust estimates of network stability.

CONCLUSIONS

Our empirical study shows that the proposed cross-validation method is useful for hyper-parameter selection (training) and comparing the quality of inferred networks between different algorithms (testing). This advancement represents a significant step forward in microbiome network analysis, providing researchers with a reliable tool for understanding complex microbial interactions. The method's applicability extends beyond microbiome studies to other fields where network inference from high-dimensional compositional data is crucial, such as gene regulatory networks and ecological food webs. Our framework establishes a new standard for validation in network inference, potentially accelerating discoveries in microbial ecology and human health.

Emergence of alternative stable states in microbial communities undergoing horizontal gene transfer

Microbial communities living in the same environment often display alternative stable states, each characterized by a unique composition of species. Understanding the origin and determinants of microbiome multistability has broad implications in environments, human health, and microbiome engineering. However, despite its conceptual importance, how multistability emerges in complex communities remains largely unknown. Here, we focused on the role of horizontal gene transfer (HGT), one important aspect mostly overlooked in previous studies, on the stability landscape of microbial populations. Combining mathematical modeling and numerical simulations, we demonstrate that, when mobile genetic elements (MGEs) only affect bacterial growth rates, increasing HGT rate in general promotes multistability of complex microbiota. We further extend our analysis to scenarios where HGT changes interspecies interactions, microbial communities are subjected to strong environmental selections and microbes live in metacommunities consisting of multiple local habitats. We also discuss the role of different mechanisms, including interspecies interaction strength, the growth rate effects of MGEs, MGE epistasis and microbial death rates in shaping the multistability of microbial communities undergoing HGT. These results reveal how different dynamic processes collectively shape community multistability and diversity. Our results provide key insights for the predictive control and engineering of complex microbiota.

Particle-Associated Bacterioplankton Communities Across the Red Sea

Pelagic particle-associated bacterioplankton play crucial roles in marine ecosystems, influencing biogeochemical cycling and ecosystem functioning. However, their diversity, composition, and dynamics remain poorly understood, particularly in unique environments such as the Red Sea. In this study, we employed eDNA metabarcoding to comprehensively characterise bacterioplankton communities associated with pelagic particles in a three-dimensional assessment spanning depths from the surface to a depth of 2300 m along the full length of the eastern Red Sea within the exclusive economic zone of the Kingdom of Saudi Arabia. Our results reveal a diverse assemblage of taxa, with Pseudomonadota, Cyanobacteriota, and Planctomycetota being the dominant phyla. We identified pronounced spatial variability in community composition among five major Red Sea geographical regions, with a third of all amplicon sequence variants being unique to the Southern Red Sea in contrast to a relatively homogenous distribution along the water column depth gradient. Our findings contribute to a deeper understanding of microbial ecology in the Red Sea and provide valuable insights into the factors governing pelagic particle-associated bacterioplankton communities in this basin.

Seasonal variation of microbial community and diversity in the Taiwan Strait sediments

Human activities and ocean currents in the Taiwan Strait exhibit significant seasonal variation, yet the response of marine microbes to ocean changes under anthropogenic and climatic stress remains unclear. Using 16S rRNA gene amplicon sequencing, we investigated the spatiotemporal dynamics and functional variations of microbial communities in sediment samples. Our findings revealed distinct seasonal patterns in microbial diversity and composition. Proteobacteria, Desulfobacterota, and Crenarchaeota dominated at the phylum level, while Candidatus Nitrosopumilus, Woeseia, and Subgroup 10 were prevalent at the genus level. Iron concentrations, heavy metals and C/N ratio were primary factors influencing microbial communities during specific seasons, whereas sulfur content, temperature fluctuations, and heavy metals shaped the entire microbial structure and diversity. Core microbial groups, including Desulfobulbus, Subgroup 10, Unidentified Latescibacterota, and Sumerlaea, played essential roles in regulating community structure and functional transitions. Marker species, such as Aliidiomarina sanyensis, Spirulina platensis, Croceimarina litoralis and Sulfuriflexus mobilis, acted as seasonal indicators. Bacteria exhibited survival strategy akin to higher organisms, encompassing process of synthesis, growth, dormancy, and disease resistance throughout the seasonal cycle. Core microbial groups and marker species in specific seasons can serve as indicators for monitoring and assessing the health of the Taiwan Strait ecosystem.

With a little help from my friends: importance of protist-protist interactions in structuring marine protistan communities in the San Pedro Channel

Marine protists form complex communities that are shaped by environmental and biological ecosystem properties, as well as ecological interactions between organisms. While all of these factors play a role in shaping protistan communities, the specific ways in which these properties and interactions influence protistan communities remain poorly understood. Fourteen years and 9 months of eukaryotic amplicon (18S-V4 rRNA gene) data collected monthly at the San Pedro Ocean Time-series (SPOT) station were used to evaluate the impacts that environmental and biological factors, and protist-protist interactions had on protistan community composition. Statistical analysis of the amplicon data revealed that seasonal patterns in protistan community composition were apparent, but that the environmental data collected through routine time-series sampling efforts could not explain most of the variability that was evident in the communities. To identify some of the protist-protist interactions that may have played a role in shaping protistan communities, ecological networks were constructed using the amplicon data and the network predictions were compared against a database of confirmed protist-protist interactions. The database comparisons revealed hundreds of established parasitic, predator-prey, photosymbiotic, and mutualistic relationships in the networks. Although many interactions were confirmed using the database, these confirmed interactions constituted only 2% of the interactions identified at the SPOT station, highlighting the need to better characterize protist-protist interactions in marine environments. Finally, the network-predicted interactions that were not found in the database were used to identify putative, novel protist-protist interactions that may have played a role in structuring the protistan communities at the SPOT station.

IMPORTANCE

Network analyses are commonly used to identify some of the ecological interactions that may be occurring between protists in the ocean; however, evaluating predictions obtained from these analyses remains difficult due to the large number of interactions that may be recovered and the limited amount of information available on protist-protist interactions in nature. In this study, ecological network analyses were conducted using data collected at the San Pedro Ocean Time-series (SPOT) station and the network predictions were compared against a database of established protist-protist interactions. These database comparisons revealed hundreds of confirmed protist-protist interactions, and thousands of putative, novel interactions that may be occurring at the SPOT station. The database comparisons carried out in this study provide a new way of evaluating network predictions and highlight the complex, yet critical role that ecological interactions play in shaping protistan community composition in marine ecosystems.

Construction and evolution of artificial reef ecosystems: Response and regulation of marine microorganisms

Artificial reefs (ARs) are an important means of improving marine ecological environments and promoting the sustainable use of marine biological resources. After AR deployment, biological communities undergo dynamic changes as species succession and shifts in community structure. As the most sensitive frontier affected by the environment, the complex and dynamic changes of microbial communities play a crucial role in the health and stability of the ecosystem. This article reviews how AR construction affects the composition and function of marine microorganisms, their contributions to ecosystem stability, and the interaction mechanisms between microbial and macroecological systems. We focus on the responses and regulatory roles of microorganisms in AR ecosystems, including changes in microbial abundance, diversity, and distribution in the environment and on reef surfaces. Additionally, we examine their roles in nutrient cycling, the carbon sequestration, and their interactions with higher trophic organisms. We identify critical knowledge gaps and research deficiencies regarding microbial community risks that need to be addressed, which provide a framework for studying the complex relationships among marine environments, microbial communities and macrobiotic communities in the process of marine ranching construction.

Spatial and temporal variation of Antarctic microbial interactions: a study around the west Antarctic Peninsula

BACKGROUND

The west Antarctic Peninsula (WAP) is a region of rapid environmental changes, with regional differences in climate warming along the north-south axis of the peninsula. Along the WAP, Palmer corresponds to a warmer region with lesser sea ice extent in the north compared to Rothera ~ 400 km to the south. Comprehensive and comparative, year-round assessments of the WAP microbial community dynamics in coastal surface waters at these two locations are imperative to understand the effects of regional climate warming variations on microbial community dynamics, but this is still lacking.

RESULTS

We report on the seasonal diversity, taxonomic overview, as well as predicted inter-and intra-domain causal effects (interactions) of the bacterial and microbial eukaryotic communities close to the Palmer station and at the Rothera time-series site between July 2013 and April 2014. Our 16S- and 18S-rRNA gene amplicon sequencing data showed that across all seasons, both bacteria and microbial eukaryotic communities were considerably different between the two sites which could be attributed to seawater temperature, and sea ice coverage in combination with sea ice type differences. Overall, in terms of biotic drivers, causal-effect modelling suggests that bacteria were stronger drivers of ecosystem dynamics at Palmer, while microbial eukaryotes played a stronger role at Rothera. The parasitic taxa Syndiniales persevered at both sites across the seasons, with Palmer and Rothera harbouring different key groups. Up to 62.3% of the negative causal effects were driven by Syndiniales at Rothera compared to only 13.5% at Palmer, suggesting that parasitism drives community dynamics at Rothera more strongly than at Palmer. Conversely, SAR11 Clade II, which was less abundant but persistent year-round at both sites, was the dominant driver at Palmer, evidenced by many (28.2% and 37.4% of positive and negative effects respectively) strong causal effects. Article note: Kindly check first page article notes are correct.

CONCLUSIONS

Our research has shed light on the dynamics of microbial community composition and correlative interactions at two sampling locations that represent different climate regimes along the WAP.

"Tire plastisphere" in aquatic ecosystems: Biofilms colonizing on tire particles exhibiting a distinct community structure and assembly compared to conventional plastisphere

Tire particles (TPs) significantly contribute to microplastics in aquatic ecosystems, which has recently attracted ecological concerns worldwide. Numerous studies have shown that biofilms on microplastics harbor unique species and harmful functions, but it remains unclear whether TPs could offer distinct niches for biofilms compared to conventional microplastics (CP). This study investigated the succession and assembly of biofilms on TPs compared with CP over 60 days. Our results showed the community structures of biofilms on TPs and CP were distinct. Intriguingly, a greater structural dissimilarity was observed between TPs-associated communities and natural biofilms compared to that between CP-associated communities and natural biofilms. This dissimilarity became more pronounced as biofilms progressed through succession. Furthermore, the bacterial community on the TPs exhibits a network of greater complexity, more stable structure, and higher activity than that on the CP, but the pattern was reversed in the eukaryotic community. Deterministic processes had a more critical impact on bacterial communities on TPs, whereas distinct stochastic processes controlled eukaryotic communities on TPs (dispersal limitation) and CP (undominated processes). Altogether, this study tentatively introduced the term "tire plastisphere" (i.e., TP-attached biofilms), emphasizing TPs could serve as more artificial microbial habitats and pose potential risks in disturbing aquatic ecology.

Seasonal recurrence and modular assembly of an Arctic pelagic marine microbiome

Deciphering how microbial communities are shaped by environmental variability is fundamental for understanding the structure and function of ocean ecosystems. While seasonal environmental gradients have been shown to structure the taxonomic dynamics of microbiomes over time, little is known about their impact on functional dynamics and the coupling between taxonomy and function. Here, we demonstrate annually recurrent, seasonal structuring of taxonomic and functional dynamics in a pelagic Arctic Ocean microbiome by combining autonomous samplers and in situ sensors with long-read metagenomics and SSU ribosomal metabarcoding. Specifically, we identified five temporal microbiome modules whose succession within each annual cycle represents a transition across different ecological states. For instance, Cand. Nitrosopumilus, Syndiniales, and the machinery to oxidise ammonia and reduce nitrite are signatures of early polar night, while late summer is characterised by Amylibacter and sulfur compound metabolism. Leveraging metatranscriptomes from Tara Oceans, we also demonstrate the consistency in functional dynamics across the wider Arctic Ocean during similar temporal periods. Furthermore, the structuring of genetic diversity within functions over time indicates that environmental selection pressure acts heterogeneously on microbiomes across seasons. By integrating taxonomic, functional and environmental information, our study provides fundamental insights into how microbiomes are structured under pronounced seasonal changes in understudied, yet rapidly changing polar marine ecosystems.

Time-decay patterns and irregular disturbance: contrasting roles of abundant and rare microbial communities in dynamic coastal seawater

Microbial communities in coastal seas experience strong environmental disturbances, yet their response patterns, especially regarding differently abundant subcommunities, remain poorly understood. Here, through 16S rRNA gene amplicon sequencing, we investigated the diversity, time-decay pattern, and assembly process of abundant, conditionally rare taxa (CRT) and rare microbial subcommunities in temperate coastal waters over 60 consecutive weeks. The abundant (50.9%) and CRT (46.1%) communities each comprised approximately half of the planktonic community, while the CRT and rare communities contributed to the extremely high species diversity. Distinct temporal heterogeneity was observed among the three fractions and was associated with taxonomic level. The abundant subcommunity exhibited time-decay patterns at all taxonomic levels, while for CRT, the pattern was found only at finer levels. In contrast, variations of the rare community loosely followed a temporal rhythm and were largely confined within a specific taxonomic range, likely raised from turnovers among closely related taxa. Determinism dominated the community assembly of the abundant fraction, while the rare one was more controlled by stochasticity that may be related to pulse terrigenous inputs and anthropogenic disturbances. The rare subcommunity with narrow niche widths likely represented a stable repository to offer episodic specialists, while the abundant taxa that exhibited broader niche widths were considered the generalists in fluctuating environments. Our study revealed the distinct strategies that abundant and rare communities adopt to maintain community stability in temporal dynamics of prokaryotic plankton in the coastal seawater.

IMPORTANCE

The relative importance of rare and abundant taxa in microbial temporal patterns remains debated. Here, we identified taxonomically associated distinct diversity modes of abundant and rare subcommunities from a year-round time-series study in dynamic coastal seawater. We highlighted the significance of the rare subcommunity in maintaining community stability by serving as a repository to offer specialists driven by stochastic processes over time. The abundant subcommunity, by contrast, contributed mainly to temporal rhythmic variations. This study expands the current understanding of the temporal dynamics and stability of coastal microbial communities by revealing distinct variation patterns of subcommunities with different abundances.

The protist community of the oligotrophic waters of the Gulf of Mexico is distinctly shaped by depth-specific physicochemical conditions during the warm season

Marine protists are key components of biogeochemical cycles and microbial food webs, which respond quickly to environmental factors. In the Gulf of Mexico (GoM), the Loop Current intensifies in summer and supplies the gulf with warm and oligotrophic waters. However, the cyclonic eddies within the GoM create favorable conditions for biological productivity by bringing nutrient-rich water to the subsurface layer. In this study, we investigated the response of the protist community to the regional physicochemical conditions, its spatial and temporal variability, the influence of mesoscale structures, and its ecological roles in the mixed layer (ML) and deep chlorophyll maximum (DCM). This is the first study to conduct a V9-18S rRNA gene survey for this community in the Mexican Exclusive Economic Zone of the GoM. The regional distribution, temporal changes, and mesoscale structures significantly affected the structure of the protist community in the ML. In contrast, only mesoscale structures significantly affected the protist community in the DCM. Different protist assemblages were also present between the ML and DCM, with the Alveolata representing ∼60% of the community in both layers, followed by haptophytes and MAST (Marine Stramenopiles) in the ML; pelagophytes and radiolarians were the more prevalent taxa in the DCM. Finally, co-occurrence analyses revealed that competition, parasitism, and predation were the potential interactions shaping these communities at both depths.

Effect of Temperature on Polyamine Oxidase Genes in Skeletonema dohrnii

In our experiments, we investigated the effect of temperature on diatom polyamine metabolism using Skeletonema dohrnii as an experimental algal species. We set three different temperature conditions for incubation and selected Skeletonema dohrnii in the exponential growth period, and analyzed basic physiological parameters, polyamine composition and content, and polyamine oxidase (PAO) gene expression at different temperatures. The results showed that low temperatures led to a decrease in growth rate, an increase in biogenic silica content, an increase in the content of putrescine and spermine, a decrease in the concentration of spermidine, and a down-regulation of PAO gene expression. In addition, high temperature led to an increase in growth rate, a significant change in the concentration of putrescine and spermine, and an increase in spermidine. These findings suggest that changes in temperature affect the growth rate of algae, low temperature increases the biogenic silica content of diatoms, different temperature stresses lead to different kinds of polyamine changes in diatoms, and the PAO gene may play a role in regulating the response of algae to temperature changes. This study lays a foundation for further exploration of the function of the PAO gene in Skeletonema dohrnii.

Differences in Biogeographic Patterns and Mechanisms of Assembly in Estuarine Bacterial and Protist Communities

As transitional ecosystems between land and sea, estuaries are characterized by a unique environment that supports complex and diverse microbial communities. A comprehensive analysis of microbial diversity and ecological processes at different trophic levels is crucial for understanding the ecological functions of estuarine ecosystems. In this study, we systematically analyzed the diversity patterns, community assembly, and environmental adaptability of bacterial and protist communities using high-throughput sequencing techniques. The results revealed a higher alpha diversity for the bacteria than for protists, and the beta diversity pattern was dominated by species turnover in both communities. In addition, the two community assemblages were shown to be dominated by deterministic and stochastic processes, respectively. Furthermore, our results emphasized the influence of the local species pool on microbial communities and the fact that, at larger scales, geographic factors played a more significant role than environmental factors in driving microbial community variation. The study also revealed differences in environmental adaptability among different microbial types. Bacteria exhibited strong adaptability to salinity, while protists demonstrated greater resilience to variations in dissolved oxygen, nitrate, and ammonium concentrations. These results suggested differences in environmental adaptation strategies among microorganisms at different trophic levels, with bacteria demonstrating a more pronounced environmental filtering effect.

Unraveling the diversity dynamics and network stability of alkaline phosphomonoesterase-producing bacteria in modulating maize yield

Phosphorus, as a nonrenewable resource, plays a crucial role in crop development and productivity. However, the extent to which straw amendments contribute to the dynamics of soil alkaline phosphomonoesterase (ALP)-producing bacterial community and functionality over an extended period remains elusive. Here, we conducted a 7-year long-term field experiment consisting of a no-fertilizer control, a chemical fertilizer treatment, and three straw (straw, straw combined with manure, and straw biochar) treatments. Our results indicated that straw amendments significantly improved the succession patterns of the ALP-producing bacterial diversity. Simultaneously, straw amendments significantly increased the network stability of the ALP-producing bacteria over time, as evidenced by higher network robustness, a higher ratio of negative to positive cohesion, and lower network vulnerability. High dynamic and stability of ALP-producing bacterial community generated high ALP activity which further increased soil Phosphorus (P) availability as well as maize productivity.

Temperature structuring of microbial communities on a global scale

Temperature is a fundamental physical constraint regulating key aspects of microbial life. Protein binding, membrane fluidity, central dogma processes, and metabolism are all tightly controlled by temperature, such that growth rate profiles across taxa and environments follow the same general curve. An open question in microbial ecology is how the effects of temperature on individual traits scale up to determine community structure and function at planetary scales. Here, we review recent theoretical and experimental efforts to connect physiological responses to the outcome of species interactions, the assembly of microbial communities, and their function as temperature changes. We identify open questions in the field and define a roadmap for future studies.

Bacterial and fungal keystone taxa play different roles in maintaining community resistance and driving soil organic carbon dynamics in response to Solidago Canadensis invasion

The invasion of alien plants has significant implications for vegetation structure and diversity, which could lead to changes in the carbon (C) input from vegetation and change the transformation and decomposition processes of C, thereby altering the dynamics of soil organic carbon (SOC) within ecosystems. Whether alien plant invasion increases the SOC stock and changes SOC fractions consistently within regional scales, and the underlying mechanisms driving these SOC dynamics remain poorly understood. This study investigated SOC dynamics by comparing the plots that suffered invasion and non-invasion of Solidago Canadensis across five ecological function areas in Anhui Province, China, considering climate, edaphic factors, vegetation, and soil microbes. The results demonstrated that the impact of S. Canadensis invasion on SOC storage was not consistent at each site in the 0-20 cm soil layer, as indicated by the range of SOC content (5.94-12.45 g kg-1) observed at non-invaded plots. Stable SOC exhibited similar response patterns with SOC to plant invasion, whereas labile SOC did not. In addition, bacterial and fungal communities were shifted in structure at each site by plant invasion. Bacterial communities exhibited greater resistance to S. Canadensis invasion than did fungal communities, as evidenced by three aspects of the resistance indices-community resistance, phylogenetic conservation, and network complexity. The mechanisms driving SOC dynamics under S. Canadensis invasion were explored using structural equation models. This revealed that fungal keystone taxa responsible for community resistance controlled stable SOC fractions. In contrast, bacterial keystone taxa had the opposite effect on labile and stable SOC. Climatic and edaphic factors were also involved in the labile and stable SOC dynamics. Overall, this study provides novel insights into the dynamics of SOC under S. Canadensis invasion on a regional scale.

Unveiling interactions mediated by B vitamins between diatoms and their associated bacteria from cocultures

Unveiling the interactions among phytoplankton and bacteria at the level of species requires axenic isolates to experimentally demonstrate their mutual effects. In this study, we describe the interactions among the diatoms Pseudo-nitzschia granii and Chaetoceros tenuissimus and their associated bacterial species, isolated from surface water of a coastal upwelling system using coculture experiments. Microalgae growth was assessed in axenic monocultures or in coculture with each of their co-isolated bacteria in the presence or absence of B vitamins. Pseudo-nitzschia granii growth was limited by B-vitamin supply, except when cultured with the bacteria Jannaschia cystaugens, which seemed to provide adequate levels of B vitamins to the diatom. Chaetoceros tenuissimus growth was reduced in the absence of B vitamins. Moreover, the growth of C. tenuissimus was stimulated by Alteromonas sp. and Celeribacter baekdonensis during the exponential growth. These results show a diversity of specific interactions between the diatoms and co-isolated bacteria, ranging from allelopathy to commensalism. Understanding how interactions between phytoplankton and bacteria modulate the structure and function of marine microbial plankton communities will contribute to a greater knowledge of plankton ecology and improve our ability to predict nutrient fluxes in marine ecosystems or the formation of blooms in a context of global change.

Impact of Viruses on Prokaryotic Communities and Greenhouse Gas Emissions in Agricultural Soils

Viruses are abundant and ubiquitous in soil, but their importance in modulating greenhouse gas (GHG) emissions in terrestrial ecosystems remains largely unknown. Here, various loads of viral communities are introduced into paddy soils with different fertilization histories via a reciprocal transplant approach to study the role of viruses in regulating greenhouse gas emissions and prokaryotic communities. The results showed that the addition of viruses has a strong impact on methane (CH4) and nitrous oxide (N2O) emissions and, to a minor extent, carbon dioxide (CO2) emissions, along with dissolved carbon and nitrogen pools, depending on soil fertilization history. The addition of a high viral load resulted in a decrease in microbial biomass carbon (MBC) by 31.4%, with changes in the relative abundance of 16.6% of dominant amplicon sequence variants (ASVs) in comparison to control treatments. More specifically, large effects of viral pressure are observed on some specific microbial communities with decreased relative abundance of prokaryotes that dissimilate sulfur compounds and increased relative abundance of Nanoarchaea. Structural equation modeling further highlighted the differential direct and indirect effects of viruses on CO2, N2O, and CH4 emissions. These findings underpin the understanding of the complex microbe-virus interactions and advance current knowledge on soil virus ecology.

Evaluating toxic impact on marine microbial community using combined genetic and phenotypic approaches

Preserving the oceans is a major challenge for the twenty-first century. In 2000, the Water Framework Directive harmonized European regulations on water management to protect and restore the good ecological status of aquatic ecosystems, including the marine environment. This study aims to address the need to understand how pollutants affect marine ecosystems, particularly microbial communities, which are vital for ecosystem balance and biogeochemical cycling. By combining genetic and phenotypic approaches, we aimed to predict the long-term ecological effects of marine pollution and develop improved management strategies. We used microcosms to expose a marine microbial community to various toxicant (anthracene, benzene, chlorpyrifos, copper chloride, and PFOA) and combined phenotypic and genetic approaches to assess i) changes in community structure, ii) phenotypic responses to pollutant, and iii) the benefits of integrating these methods to better evaluate the impact of pollutants on microbial communities and ecosystem services. The obtained results highlight a certain functional resilience despite a significant effect on genetic diversity. Moreover, only specific exposure conditions, such as higher pollutant concentrations, appear to significantly affect ecosystem functions. Leveraging this knowledge, the future challenge will be to develop a straightforward biosensor to estimate and predict the impact of pollutants on these ecosystems, in order to better protect them.

Bioavailability of dissolved organic matter (DOM) derived from seaweed Gracilaria lemaneiformis meditated by microorganisms

Seaweed Gracilaria lemaneiformis, a significant oceanic primary producer, releases substantial dissolved organic matter (DOM) during growth and decay, potentially impacting coastal organic carbon reservoirs and microbial communities. This study aimed to investigate the bioavailability of Gracilaria-derived DOM and its interactions with microbial communities. Laboratory experiments introduced Gracilaria-derived DOM into natural seawater, tracking variations in DOM composition, microbial structure, and eight extracellular enzyme activities over 168 h. The results indicated a rapid breakdown of dissolved organic carbon, nitrogen, and phosphorus, representing 48 % to 90 % of their total concentrations within 168 h, highlighting the high DOM bioavailability. Tryptophan substances were identified as the primary components of Gracilaria-derived DOM, being highly labile and utilized by microorganisms. Within the initial 0-12 h of DOM influx, Proteobacteria significantly increased and dominated in bacterial community, while after 48 h, as DOM decomposed, Desulfobacterota became the dominant group. The labile DOM stimulated bacteria, particularly Proteobacteria, to release substantial extracellular enzymes that peaked within the first 12 h. Subsequent substrate depletion led to decreased enzyme activities. Positive correlations were observed among bacterial abundance, enzyme activities, and tryptophan substances, emphasizing the intricate interplay among microbial communities, labile DOM, and extracellular enzymes. This study underscores the high bioavailability of Gracilaria-derived DOM and its interactions with microbial communities in nearshore environments.

Revealing the intricate temporal dynamics and adaptive responses of prokaryotic and eukaryotic microbes in the coastal South China Sea

This comprehensive two-year investigation in the coastal South China Sea has advanced our understanding of marine microbes at both community and genomic levels. By combining metagenomics and metatranscriptomics, we have revealed the intricate temporal dynamics and remarkable adaptability of microbial communities and phytoplankton metagenome-assembled genomes (MAGs) in response to environmental fluctuations. We observed distinct seasonal shifts in microbial community composition and function: cyanobacteria were predominant during warmer months, whereas photosynthetic protists were more abundant during colder seasons. Notably, metabolic marker KOs of photosynthesis were consistently active throughout the year, underscoring the persistent role of these processes irrespective of seasonal changes. Our analysis reveals that environmental parameters such as temperature, salinity, and nitrate concentrations profoundly influence microbial community composition, while temperature and silicate have emerged as crucial factors shaping their functional traits. Through the recovery and analysis of 37 phytoplankton MAGs, encompassing nine prokaryotic cyanobacteria and 28 eukaryotic protists from diverse phyla, we have gained insights into their genetic diversity and metabolic capabilities. Distinct profiles of photosynthesis-related pathways including carbon fixation, carotenoid biosynthesis, photosynthesis-antenna proteins, and photosynthesis among the MAGs indicated their genetic adaptations to changing environmental conditions. This study not only enhances our understanding of microbial dynamics in coastal marine ecosystems but also sheds light on the ecological roles and adaptive responses of different microbial groups to environmental changes.

Game-Theoretic Flux Balance Analysis Model for Predicting Stable Community Composition

Models for microbial interactions attempt to understand and predict the steady state network of inter-species relationships in a community, e.g. competition for shared metabolites, and cooperation through cross-feeding. Flux balance analysis (FBA) is an approach that was introduced to model the interaction of a particular microbial species with its environment. This approach has been extended to analyzing interactions in a community of microbes; however, these approaches have two important drawbacks: first, one has to numerically solve a differential equation to identify the steady state, and second, there are no methods available to analyze the stability of the steady state. We propose a game theory based community FBA model wherein species compete to maximize their individual growth rate, and the state of the community is given by the resulting Nash equilibrium. We develop a computationally efficient method for directly computing the steady state biomasses and fluxes without solving a differential equation. We also develop a method to determine the stability of a steady state to perturbations in the biomasses and to invasion by new species. We report the results of applying our proposed framework to a small community of four E. coli mutants that compete for externally supplied glucose, as well as cooperate since the mutants are auxotrophic for metabolites exported by other mutants, and a more realistic model for a gut microbiome consisting of nine species.

Carbon flow allocation patterns of CH4, CO2, and biomass production vary with sewage and sediment microbial and biochemical factors in the anaerobic sewer environment

Understanding the carbon (C) fate in municipal sewers is imperative for optimizing current sewer-C-degradation control and treatment efficiency, aligning with China's C-neutrality strategy in determining the exact C budget of the wastewater system. This study used laboratory batch tests mimicking the anaerobic sewer environment and sewage-sediment stratification to evaluate C flow allocation (CFA) patterns in response to biotic and abiotic variables. We quantified the C equivalent mass (CEM) and used absolute quantitative 16S rRNA gene amplicon sequencing to characterize the microbiome. The substantial methane production (CH4, 17.2%-18.8%) required both activated sediment and exogenous C, while biomass production (BP, 63.1%-74.9%) formed C sink predominated as the main CFA direction under the stratified state. This was supported by the high diversity, interspecific interactions, and metabolic capacity of the sediment microbiome. However, CH4 and BP patterns demonstrated non-synchronicity and opposite dynamic characteristics. Carbon dioxide (CO2, 64.0%-81.3%) production dominated the sewage CFA. The absolute abundance of the sediment microbiome, which was 5.6 times higher than that of the sewage, exhibited a strong increase in magnitude across the phases. It was primarily associated with biomass growth and N metabolism, whereas sewage showed differentiated and competing communities and appeared to act mainly as the exogenous C sources. We constructed a binary quadratic linear model revealing the non-linear relationship between ACK activity, DOC degradation rate, and CEMCH4 rate; the former maintained low CH4 production when the available substrate was insufficient. The influence of N and S factors on the CFA is complex and multi-faceted. These findings highlight the importance of further investigations into the process-based framework of the sewer C budget, focusing on the C source-emission-sink functions and mass balance.

Seasonal variations of microbial communities and viral diversity in fishery-enhanced marine ranching sediments: insights into metabolic potentials and ecological interactions

BACKGROUND

The ecosystems of marine ranching have enhanced marine biodiversity and ecological balance and have promoted the natural recovery and enhancement of fishery resources. The microbial communities of these ecosystems, including bacteria, fungi, protists, and viruses, are the drivers of biogeochemical cycles. Although seasonal changes in microbial communities are critical for ecosystem functioning, the current understanding of microbial-driven metabolic properties and their viral communities in marine sediments remains limited. Here, we employed amplicon (16S and 18S) and metagenomic approaches aiming to reveal the seasonal patterns of microbial communities, bacterial-eukaryotic interactions, whole metabolic potential, and their coupling mechanisms with carbon (C), nitrogen (N), and sulfur (S) cycling in marine ranching sediments. Additionally, the characterization and diversity of viral communities in different seasons were explored in marine ranching sediments.

RESULTS

The current study demonstrated that seasonal variations dramatically affected the diversity of microbial communities in marine ranching sediments and the bacterial-eukaryotic interkingdom co-occurrence networks. Metabolic reconstruction of the 113 medium to high-quality metagenome-assembled genomes (MAGs) was conducted, and a total of 8 MAGs involved in key metabolic genes and pathways (methane oxidation - denitrification - S oxidation), suggesting a possible coupling effect between the C, N, and S cycles. In total, 338 viral operational taxonomic units (vOTUs) were identified, all possessing specific ecological characteristics in different seasons and primarily belonging to Caudoviricetes, revealing their widespread distribution and variety in marine sediment ecosystems. In addition, predicted virus-host linkages showed that high host specificity was observed, with few viruses associated with specific hosts.

CONCLUSIONS

This finding deepens our knowledge of element cycling and viral diversity in fisheries enrichment ecosystems, providing insights into microbial-virus interactions in marine sediments and their effects on biogeochemical cycling. These findings have potential applications in marine ranching management and ecological conservation. Video Abstract.

Anthropogenic activity shapes the assemble and co-occurrence pattern of microbial communities in fishing harbors around the Bohai economic circle

This study aimed to elucidate the effects of coastal environmental stress on the composition of sediment bacterial communities and their cooccurrence patterns in fishing harbors around the Bohai Economic Circle, China. Compared with the natural sea area, fishing harbors contained higher levels of organic pollution (organic pollution index = 0.12 ± 0.026) and considerably reduced bacterial richness and evenness. The distributions of sediment microbial communities clustered along the pollutant concentration gradients across fishing harbors. Betaproteobacteria dominated (76%) organically polluted fishing harbors, which were mostly disturbed by anthropogenic activities. However, the harbors also revealed the absence of numerous pathogenic (Coxiella and Legionella) and photosynthetic (Synechococcus and Leptolyngbya) bacteria. Abundant genera, including Thiobacillus and Arenimonas, exhibited a positive correlation with total phosphorus and a negative correlation with total nitrogen in sediments. Meanwhile, Sulfurovum, Psychrobacter, and Woeseia showed the opposite trend. Pollutant accumulation and anthropogenic activities caused the decrease in the sediment microbial diversity and dispersal ability and promoted convergent evolution. Severely polluted harbors with simplified cooccurrence networks revealed the presence of destabilized microbial communities. In addition, the modularity of bacterial networks decreased with organic pollution. Our results provide important insights into the adjustment mechanism of microbial communities to community organization and functions under environmental pollution stress. Overall, this study enhanced our understanding of how microbial communities in coastal sediments adapted and survived amidst anthropogenic activities like oily effluent discharges from large ships, wash water, domestic sewage, garbage, and fisheries wastes. It also examined their resilience to future contamination.

Cinnamoyl lipids as novel signaling molecules modulate the physiological metabolism of cross-phylum microorganisms

Signaling systems of microorganisms are responsible for regulating the physiological and metabolic processes and also play vital roles in the communications of cells. Identifying signaling molecules mediating the cross-talks is challenging yet highly desirable for comprehending the microbial interactions. Here, we demonstrate that a pathogenic Gram-negative Chromobacterium violaceum exerts significant influence on the morphological differentiation and secondary metabolism of Gram-positive Streptomyces. The physiological metabolisms are directly modulated by three novel cinnamoyl lipids (CVCL1, 2, and 3) from C. violaceum CV12472, whose biosynthesis is under the control of N-acylhomoserine lactone signaling system. Furthermore, a receptor of CVCLs in Streptomyces ansochromogenes 7100 is determined to be SabR1, the cognate receptor of γ-butenolide signaling molecules. This study reveals an unprecedented mode of microbial interactions, and the quorum sensing signaling systems in these two groups of bacteria can be bridged via CVCLs, suggesting that CVCLs can modulate the physiological metabolism of cross-phylum microorganisms.

Effect of harvesting season and location on the microbial quality and community composition of the edible sea urchin (Echinus esculentus) gonads

Despite the crucial role of microbial community composition in the quality and stability of seafood, little emphasis has been given to the microbiota profile of sea urchin gonads. This study investigates the microbial quality and community composition of sea urchin gonads (Echinus esculentus) as a function of harvesting season (autumn, winter, spring, and summer) and location (one site proximal to urban activity areas while the other is located in open water close to the coastline). Significant season-dependent variations were found in psychrotrophic and aerobic plate counts, with higher counts in summer, followed by autumn, spring, and winter. H2S-producing bacteria and Pseudomonas spp. counts were unaffected by harvesting season or location. Sea urchin gonad microbial composition proved resilient and dynamic, primarily shaped by seasonal variations, and minimally influenced by location. Winter and spring samples exhibited higher diversity than autumn and summer. Key genera like Pseudomonas, Psychromonas, Vibrio, Chryseobacterium, Shewanella, and Photobacterium varied seasonally. Pseudomonas, Vibrio, and Photobacterium are crucial in assessing microbial quality and safety due to their roles as specific spoilage organisms (SSOs) and, in some cases, human pathogens. Though relative abundances differed slightly between locations, harvesting location did not notably impact microbial community shaping in gonads. However, the results suggest that harvesting locations near areas with urban activity may lead to contamination with specific bacterial species, possibly due to water quality variations. These findings emphasize the importance of considering seasonality when evaluating sea urchin gonad microbial quality. Identifying key genera enhances insights into potential SSOs and human pathogens, enhancing food safety considerations in the consumption of raw or lightly processed sea urchin gonads and guiding the development of preservation methods to extend shelf life.

Distinct Communities of Bacteria and Unicellular Eukaryotes in the Different Water Masses of Cretan Passage Water Column (Eastern Mediterranean Sea)

Elucidating marine microbiota diversity and dynamics holds significant importance due to their role in maintaining vital ecosystem functions and services including climate regulation. This work aims to contribute in the understanding of microbial ecology and networking in one of the world's most understudied marine regions, the Eastern Mediterranean Sea. High-throughput 16S and 18S rRNA gene sequencing analysis was applied to study the diversity of bacteria and unicellular eukaryotes in the different water masses of the Cretan Passage during two seasonally-different sampling expeditions. We assumed that microbial associations differ between the surface and deepwater masses and created co-occurrence networks to evaluate this hypothesis. Our results unveiled vertical variations in both bacterial and unicellular eukaryotic diversity with species fluctuations indicative of seasonality being recorded in the surface water mass. Heterotrophic taxa and grazers related to organic matter degradation and nutrient cycling were enriched in the deepest water layers. Moreover, surface waters presented a higher number of microbial associations indicating abundant ecological niches compared to the deepest layer, possibly related to the lack of bottom-up resources in the oligotrophic deep ocean. Overall, our data provide insight in a heavily stressed, yet underexplored, marine area that requires further research to unravel the ecological roles of marine microbes. To our knowledge, this is the first study that combines molecular biology tools to provide data on both planktic prokaryotes and unicellular eukaryotes across the different water masses in this marine region of the Eastern Mediterranean basin.

Community organization and network complexity and stability: contrasting strategies of prokaryotic versus eukaryotic microbiomes in the Bohai Sea and Yellow Sea

Unraveling the effects of spatial gradients on microbiome assembly and association is a challenging topic that remains understudied in the coastal ecosystem. Here, we aimed to investigate the effects of spatial variation on the network complexity and stability of plankton microbiomes in the Bohai Sea and Yellow Sea. These seas serve as spawning and nursery grounds for economically important fisheries valued at billions of dollars annually. Environmental heterogeneity structures microbial communities into distinct spatial patterns, leading to complex direct/indirect relationships and broader ecological niches of bacterioplankton compared to microeukaryotic communities. Interestingly, salinity gradients positively influenced the richness of rare subgroups of bacterioplankton, while the rare microeukaryotic subgroups showed an opposite trend. Abundant subgroups of prokaryotic/eukaryotic microbiomes exhibited greater environmental niche breadth and lower phylogenetic distance compared to the rare subgroups. Stochastic processes contributed greatly to microbiome dynamics, and deterministic processes governed the bacterioplankton organization with a lower phylogenetic turnover rate. Compared to microeukaryotes, bacterioplankton exhibit higher network modularity, complexity, and robustness and lower fragmentation, and vulnerability. These observations offer vital insights into the anti-interference ability and resistance of plankton microbiomes in response to environmental gradients in terms of organization and survival strategy as well as their adaptability to environmental disturbances.IMPORTANCEAn in-depth understanding of community organization and stability of coastal microbiomes is crucial to determining the sustainability of marine ecosystems, such as the Bohai Sea and Yellow Sea. Distinct responses between prokaryotic and eukaryotic microbiomes to spatial heterogeneity were observed in terms of geographical distribution, phylogenetic distance, niche breadth, and community assembly process. Environmental variations are significantly correlated with the dynamics of rare eukaryotic plankton subcommunities compared to prokaryotic plankton subcommunities. Deterministic processes shaped prokaryotic plankton community organization with a lower phylogenic turnover rate. Rare subgroups had noticeably higher phylogenetic distance and lower niche breadth than the corresponding abundant subgroups. Prokaryotic microbiomes had higher molecular network complexity and stability compared to microeukaryotes. Results presented here show how environmental gradients alter both the geographical characteristics of the microbial organization in coastal seas and also their co-occurrence network complexity and stability and thus have critical implications for nutrient and energy cycling.

Ocean acidification alters microeukaryotic and bacterial food web interactions in a eutrophic subtropical mesocosm

Ocean acidification (OA) is known to influence biological and ecological processes, mainly focusing on its impacts on single species, but little has been documented on how OA may alter plankton community interactions. Here, we conducted a mesocosm experiment with ambient (∼410 ppmv) and high (1000 ppmv) CO2 concentrations in a subtropical eutrophic region of the East China Sea and examined the community dynamics of microeukaryotes, bacterioplankton and microeukaryote-attached bacteria in the enclosed coastal seawater. The OA treatment with elevated CO2 affected taxa as the phytoplankton bloom stages progressed, with a 72.89% decrease in relative abundance of the protist Cercozoa on day 10 and a 322% increase in relative abundance of Stramenopile dominated by diatoms, accompanied by a 29.54% decrease in relative abundance of attached Alphaproteobacteria on day 28. Our study revealed that protozoans with different prey preferences had differing sensitivity to high CO2, and attached bacteria were more significantly affected by high CO2 compared to bacterioplankton. Our findings indicate that high CO2 changed the co-occurrence network complexity and stability of microeukaryotes more than those of bacteria. Furthermore, high CO2 was found to alter the proportions of potential interactions between phytoplankton and their predators, as well as microeukaryotes and their attached bacteria in the networks. The changes in the relative abundances and interactions of microeukaryotes between their predators in response to high CO2 revealed in our study suggest that high CO2 may have profound impacts on marine food webs.

Effects of long-term continuous cultivation on the structure and function of soil bacterial and fungal communities of Fritillaria Cirrhosa on the Qinghai-Tibetan Plateau

Fritillaria cirrhosa, an endangered medicinal plant in the Qinghai-Tibet Plateau, is facing resource scarcity. Artificial cultivation has been employed to address this issue, but problems related to continuous cultivation hinder successful transplantation. Imbalanced microbial communities are considered a potential cause, yet the overall changes in the microbial community under continuous cropping systems remain poorly understood. Here, we investigated the effects of varying durations of continuous cropping on the bacterial and fungal communities, as well as enzymatic activities, in the rhizospheric soil of F. cirrhosa. Our findings revealed that continuous cropping of F. cirrhosa resulted in soil acidification, nutrient imbalances, and increased enzyme activity. Specifically, after 10 years of continuous cropping, there was a notable shift in the abundance and diversity (e.g., Chao1 index) of soil bacteria and fungi. Moreover, microbial composition analyses revealed a significant accumulation of harmful microorganisms associated with soil-borne diseases (e.g., Luteimonas, Parastagonospora, Pseudogymnoascus) in successively cropped soils, in contrast to the significant reduction of beneficial microorganisms (e.g., Sphingomonas, Lysobacter, Cladosporium) that promote plant growth and development and protect against diseases such as Fusarium sp.These changes led to decreased connectivity and stability within the soil microbial community. Structural equation modeling and redundancy analysis revealed that alkaline hydrolytic nitrogen and available phosphorus directly influenced soil pH, which was identified as the primary driver of soil microbial community changes and subsequently contributed to soil health deterioration. Overall, our results highlight that soil acidification and imbalanced rhizosphere microbial communities are the primary challenges associated with continuous cropping of F. cirrhosa. These findings establish a theoretical foundation for standardized cultivation practices of F. cirrhosa and the bioremediation of continuously cultivated soils.

Disentangling the factors defining Bacillus subtilis group species abundance in natural soils

Bacillus subtilis is ubiquitously and broadly distributed in various environments but is mostly isolated from soil. Given that B. subtilis is known as a plant growth-promoting rhizobacterium in agriculture, we aimed to describe the natural distribution of this species and uncover how biotic and abiotic factors affect its distribution. When comparing different soils, we discovered that B. subtilis group species are most abundant in grasslands but can rarely be isolated from forest soil, even if the soil sample sites are situated in proximity. Differential analysis revealed that spore-forming bacteria exhibited enrichments in the grassland, suggesting niche overlap or synergistic interactions leading to the proliferation of certain Bacillus species in grassland environments. Network analysis further revealed that Bacillus and other Bacillota established a densely interconnected hub module in the grassland, characterised by positive associations indicating co-occurrence, a pattern not observed in the forest soil. Speculating that this difference was driven by abiotic factors, we combined amplicon sequencing with physico-chemical analysis of soil samples and found multiple chemical variables, mainly pH, to affect microbial composition. Our study pinpoints the factors that influence B. subtilis abundance in natural soils and, therefore, offers insights for designing B. subtilis-based biocontrol products in agricultural settings.

Urbanization reduces the stability of soil microbial community by reshaping the diversity and network complexity

Rapid urbanization considerably alters soil environment, biodiversity, and stability of terrestrial ecosystems. Soil microbial community, a key component of global biodiversity, plays a pivotal role in ecosystem stability and is highly vulnerable to urbanization. However, effects of urbanization on the diversity, stability, and network structure of soil microbial community remain poorly understood. Herein, we investigated the diversity and stability of soil microbial communities, including bacteria, fungi, and protists, across three regions with different levels of urbanization-urban, suburb, and ecoregion-using high-throughput sequencing techniques. Our results revealed that urbanization led to a notable decrease in the alpha diversity of soil microbial community, causing a significant reduction in soil stability, as assessed by the average variation degree (AVD). The loss of stability was linked to the diminished alpha diversity of the soil fungal and protistan communities, along with weakened interactions among bacteria, fungi, and protists. Notably, the majority of keystone species identified through network analysis were classified as bacteria (Proteobacteria) and displayed a strong positive correlation with the environmental factors influencing AVD. This highlights that the variability of bacteria and the immutability of fungi and protists are important to sustain soil microbial stability. Furthermore, structural equation models indicated that protistan diversity primarily drove soil microbial stability across all regions studied. In the suburban and ecoregion areas, soil microbial stability was directly influenced by the soil properties, bacterial diversity, and keystone species, as well as indirectly affected by heavy metals. These results underscore how urbanization can reduce the stability of soil microbial community via declined diversity and network complexity, whereas the establishment of ecoregions maybe contribute to preserve the diversity and stability of soil microbial community.

Seasonal and interannual variability of the free-living and particle-associated bacteria of a coastal microbiome

Marine microbial communities differ genetically, metabolically, and ecologically according to their lifestyle, and they may respond differently to environmental changes. In this study, we investigated the seasonal dynamics of bacterial assemblies in the free-living (FL) and particle-associated (PA) fractions across a span of 6 years in the Blanes Bay Microbial Observatory in the Northwestern Mediterranean. Both lifestyles showed marked seasonality. The trends in alpha diversity were similar, with lower values in spring-summer than in autumn-winter. Samples from both fractions were grouped seasonally and the percentage of community variability explained by the measured environmental variables was comparable (32% in FL and 31% in PA). Canonical analyses showed that biotic interactions were determinants of bacterioplankton dynamics and that their relevance varies depending on lifestyles. Time-decay curves confirmed a high degree of predictability in both fractions. Yet, 'seasonal' Amplicon Sequence Variants (ASVs) (as defined by Lomb Scargle time series analysis) in the PA communities represented 46% of the total relative abundance while these accounted for 30% in the FL fraction. These results demonstrate that bacteria inhabiting both fractions exhibit marked seasonality, highlighting the importance of accounting for both lifestyles to fully comprehend the dynamics of marine prokaryotic communities.

Algal methylated compounds shorten the lag phase of Phaeobacter inhibens bacteria

The lag phase is key in resuming bacterial growth, but it remains underexplored particularly in environmental bacteria. Here we use transcriptomics and 13C-labelled metabolomics to show that the lag phase of the model marine bacterium Phaeobacter inhibens is shortened by methylated compounds produced by the microalgal partner, Emiliania huxleyi. Methylated compounds are abundantly produced and released by microalgae, and we show that their methyl groups can be collected by bacteria and assimilated through the methionine cycle. Our findings underscore the significance of methyl groups as a limiting factor during the lag phase and highlight the adjustability of this growth phase. In addition, we show that methylated compounds, typical of photosynthetic organisms, prompt diverse reductions in lag times in bacteria associated with algae and plants, potentially favouring early growth in some bacteria. These findings suggest ways to accelerate bacterial growth and underscore the significance of studying bacteria within an environmental context.

Enhanced nutrient supply promotes mutualistic interactions between cyanobacteria and bacteria in oligotrophic ocean

Cyanobacteria can form complex interactions with heterotrophic microorganisms, but this relationship is susceptible to nutrient concentrations. Disentangling the cyanobacteria-bacteria interactions in relation to nutrient supply is essential to understanding their roles in geochemical cycles under global change. We hypothesize that enhanced nutrient supply in oligotrophic oceans can promote interactions among cyanobacteria and bacteria. Therefore, we investigated the planktonic bacteria and their interactions with cyanobacteria in relation to elevated nutrients caused by enhanced upwelling around a shallow and a deep seamount in the tropical western Pacific Ocean. We found obviously higher complexity of network occurred with significantly more cyanobacteria in the deep chlorophyll maximum layer of the shallow seamount when compared with that of the deep seamount. Cyanobacteria can shape bacterial interaction and community evenness in response to relatively high nutrient concentrations. The effects of the nutrients on cyanobacteria-related networks were further estimated based on the Tara Oceans data. Statistical analyses further showed a facilitative effect of nitrate concentrations on cyanobacteria-bacteria mutualistic interactions in the global oligotrophic ocean. By analysing the Tara Ocean macrogenomic data, we detected functional genes related to cyanobacteria-bacteria interactions in all samples, indicating the existence of a mutualistic relationship. Our results reveal cyanobacteria-bacteria interaction in response to nutrient elevation in oligotrophic ocean and highlight the potentially negative effects of global change on the bacterial community from the view of the bio-interaction.