Adaptation of intertidal biofilm communities is driven by metal ion and oxidative stresses

Molecular insights into cobalt homeostasis in estuarine microphytobenthos: A meta-transcriptomics and biogeochemical approach

Meta-transcriptomics data supported by biofilm physico-chemical parameters unravelled the molecular and biochemical processes utilized by multicomponent intertidal biofilms to endure cobalt toxicity. Findings indicated activation of influx (BtuB, ABC-type transporters) and efflux pumps (RND, CZC) to maintain metal ion homeostasis. Enhanced specific activity of antioxidant enzymes namely catalases and peroxidases (KatG, SodA) mitigated oxidative damage. Heightened synthesis of capsular polysaccharide components, specifically uronic acid and carbohydrate via PEP-CTERM sorting system, wzy pathway and glycosyltransferases protected biofilms against cobalt exposure. Despite chlorophyll biosynthesis genes being upregulated, metal toxicity impeded chlorophyll replenishment. Principal pathways associated with iron acquisition (AfuA), energy metabolism (AtpG), general metabolic activities (FruK, NifD, coABC) and central dogma regulation (DPS, AsrR, RRM) were activated to combat cobalt toxicity. This investigation offered novel insights into the regulatory network employed by intertidal microphytobenthic communities for maintaining cobalt homeostasis and underlined the basis for their application as biomarkers for estuarine cobalt pollution.

Changes in the assembly and functional adaptation of endophytic microbial communities in Amorphophallus species with different levels of resistance to necrotrophic bacterial pathogen stress

Pcc is one of the key pathogenic factors responsible for destructive soft rot in konjac. To date, the assembly and functional adaptation of the plant endophytic microbiome under Pcc stress remain poorly understood. Here, we found that Pcc stress leads to rapid reorganization of the endogenous microbiome in multiple organs of both susceptible and resistant konjac plants. Under Pcc stress, the negative interactions within the bacterial-fungal interdomain network intensified, suggesting an increase in ecological competition between bacterial and fungal taxa. We further discovered that the relative abundance dynamics of the classes Dothideomycetes and Sordariomycetes, as core fungal taxa, changed in response to Pcc stress. By isolating culturable microorganisms, we demonstrated that 46 fungal strains strongly inhibited the growth of Pcc. This implies that endophytic fungal taxa in konjac may protect the host plant through ecological competition or by inhibiting the growth of pathogenic bacteria. Metagenomic analysis demonstrated that microbial communities associated with resistant Amorphophallus muelleri exhibited unique advantages over susceptible Amorphophallus konjac in enhancing environmental adaptability, regulating plant immune signaling, strengthening cell walls, and inducing defense responses. Our work provides important evidence that endophytic fungal taxa play a key role in the host plant's defense against necrotizing bacterial pathogens.

Impacts of sulfamethoxazole on heterotrophic nitrification-aerobic denitrification bacteria and its response strategies: Insights from physiology to proteomics

The effects of sulfonamide antibiotics on heterotrophic nitrification-aerobic denitrification (HN-AD) and the response mechanisms of HN-AD bacteria are not fully understood. This study investigated the physiological changes and proteomic responses of the HN-AD bacteria Pseudomonas stutzeri (P. stutzeri) under varying concentrations of sulfamethoxazole (SMX). Results indicated that SMX inhibited the growth and HN-AD performance of P. stutzeri in a concentration-dependent manner. SMX exposure led to decreased motility, reduced electron transfer system activity, and diminished activities of key denitrifying enzymes, accompanied by increased levels of intracellular reactive oxygen species and compromised cell membrane integrity. Additionally, the production of extracellular polymeric substances and self-aggregation ability of P. stutzeri initially increased and then decreased with rising SMX concentrations. Proteomic analysis revealed that SMX primarily suppressed pathways involved in bacterial chemotaxis, ABC transporters, two-component systems, fatty acid metabolism, and nitrogen metabolism. In response, P. stutzeri upregulated pathways associated with starch and sucrose metabolism, carotenoid biosynthesis, styrene degradation, O-antigen nucleotide sugar biosynthesis, and the pentose phosphate pathway. These findings provide insights into the effects of sulfonamide antibiotics on HN-AD bacteria and their response mechanisms, offering references for the application of HN-AD processes in treating antibiotic-containing wastewater.

Warming and polymetallic stress induce proteomic and physiological shifts in the neurotoxic Alexandrium pacificum as possible response to global changes

Harmful Algal Blooms involving the dinoflagellate Alexandrium pacificum continue to increase in ecosystems suffering the climate warming and anthropogenic pressure. Changes in the total proteome and physiological traits of the Mediterranean A. pacificum SG C10-3 strain were measured in response to increasing temperature (24 °C, 27 °C, 30 °C) and trace metal contamination (Cu2+, Pb2+, Zn2+, Cd2+). Warming reduced the cell densities and maximal growth rate (μmax), but the strain persisted at 30 °C with more large cells. The polymetallic stress increased cell sizes, reduced cell growth at 24 °C-27 °C and it increased this at 30 °C. Toxin profiles showed a predominance of GTX4 (32-38 %), then C2 (11-34 %) or GTX6 (18-24 %) among the total Paralytic Shellfish Toxins, however these were modified under warming, showing increased contents in GTX1 (among the most toxic), GTX5, C1 and NeoSTX, while dc-NeoSTX and STX (among the most toxic) only appeared at 30 °C. Under polymetallic contamination, warming also increased contents in GTX5 and NeoSTX. In contrast, polymetallic stress, or warming had harmful effects on C2 contents. Proteins were more quantitatively produced by A. pacificum SG C10-3 under warming in accordance with the high levels of up-regulated proteins found in the total proteome in this condition. Polymetallic stress, only or combined with warming, led to low proteomic modifications (1 % or 4 %), whereas warming induced strong 52 % modified proteomic response, mainly based on up-regulated proteins involved in photosynthesis (light harvesting complex protein), carbohydrate metabolism (arylsulfatase) and translation (ribosomal proteins), and with the lesser down-regulated proteins principally associated with the lipid metabolism (type I polyketide synthase). Our results show that warming triggers a strong up-regulated A. pacificum SG C10-3 proteomic response, which, coupled to modified cell sizes and toxin profiles, could help it to withstand stress conditions. This could presage the success of A. pacificum in anthropized ecosystems submitted to global warming in which this dinoflagellate also might be more toxic.

The metabolic characteristics and environmental adaptations of the intertidal bacterium Palleronia sp. LCG004

The intertidal zone, a dynamic interface of marine, atmospheric, and terrestrial ecosystems, exposes microorganisms to rapid shifts in temperature, salinity, and oxidative stress. Strain LCG004, representing a novel Palleronia species, was isolated from the Lu Chao Harbor's intertidal seawater in the Western Pacific Ocean. The genome of the organism reveals its metabolic versatility, enabling the utilization of various organic substrates-ranging from organic acids, amino acids, to sugars, and encompassing complex carbohydrates-as well as adept handling of inorganic nutrients, thereby highlighting its significant role in the cycling of nutrients. The strain is equipped with multiple osmoprotectant transporters, deoxyribodipyrimidine photo-lyase, and a comprehensive antioxidant defense system, featuring with multiple catalases, peroxidases, and superoxide dismutases, enabling it to withstand ever-changing environmental conditions, UV radiation, and oxidative challenges. Notably, LCG004 exhibited enhanced growth and cell aggregation under oligotrophic conditions, promoted by light exposure, underscoring the significant influence of light on its morphological and physiological attributes. This study elucidates strain LCG004's metabolic characteristics and ecological potential, and offers insights into its contributions to biogeochemical cycles and survival strategies in one of nature's most fluctuating environments.

Genomic Features and Antimicrobial Activity of Phaeobacter inhibens Strains from Marine Biofilms

Members of the genus Phaeobacter are widely distributed in the marine environment and are known for their ability to produce tropodithietic acid (TDA). Studies investigating the genomic and metabolic features of Phaeobacter strains from marine biofilms are sparse. Here, we analyze the complete genomes of 18 Phaeobacter strains isolated from biofilms on subtidal stones, with the aim of determining their potential to synthesize secondary metabolites. Based on whole-genome comparison and average nucleotide identity calculation, the isolated bacteria are classified as novel strains of Phaeobacter inhibens. Further analysis reveals a total of 153 biosynthetic gene clusters, which are assigned to 32 gene cluster families with low similarity to previously published ones. Complete TDA clusters are identified in 14 of the 18 strains, while in the other 4 strains the TDA clusters are rather incomplete and scattered across different chromosome and plasmid locations. Phylogenetic analysis suggests that their presence or absence may be potentially attributed to horizontal gene transfer. High-performance liquid chromatography-mass spectrometry analysis demonstrates the production of TDA in all the examined strains. Furthermore, the Phaeobacter strains have strong antibacterial activity against the pathogenic strain Vibrio owensii ems001, which is associated with acute hepatopancreatic necrosis in South American white shrimp. Altogether, this study ameliorates our knowledge of marine biofilm-associated Phaeobacter and offers new avenues for exploiting marine antimicrobial agents.

Microbial community and network responses across strong environmental gradients: How do they compare with macroorganisms?

The way strong environmental gradients shape multispecific assemblages has allowed us to examine a suite of ecological and evolutionary hypotheses about structure, regulation and community responses to fluctuating environments. But whether the highly diverse co-occurring microorganisms are shaped in similar ways as macroscopic organisms across the same gradients has yet to be addressed in most ecosystems. Here, we characterize intertidal biofilm bacteria communities, comparing zonation at both the "species" and community levels, as well as network attributes, with co-occurring macroalgae and invertebrates in the same rocky shore system. The results revealed that the desiccation gradient has a more significant impact on smaller communities, while both desiccation and submersion gradients (surge) affect the larger, macroscopic communities. At the community level, we also confirmed the existence of distinct communities within each intertidal zone for microorganisms, similar to what has been previously described for macroorganisms. But our results indicated that dominant microbial organisms along the same environmental gradient exhibited less differentiation across tidal levels than their macroscopic counterparts. However, despite the substantial differences in richness, size and attributes of co-occurrence networks, both macro- and micro-communities respond to stress gradients, leading to the formation of similar zonation patterns in the intertidal rocky shore.

Copiotrophy in a Marine-Biofilm-Derived Roseobacteraceae Bacterium Can Be Supported by Amino Acid Metabolism and Thiosulfate Oxidation

Copiotrophic bacteria that respond rapidly to nutrient availability, particularly high concentrations of carbon sources, play indispensable roles in marine carbon cycling. However, the molecular and metabolic mechanisms governing their response to carbon concentration gradients are not well understood. Here, we focused on a new member of the family Roseobacteraceae isolated from coastal marine biofilms and explored the growth strategy at different carbon concentrations. When cultured in a carbon-rich medium, the bacterium grew to significantly higher cell densities than Ruegeria pomeroyi DSS-3, although there was no difference when cultured in media with reduced carbon. Genomic analysis showed that the bacterium utilized various pathways involved in biofilm formation, amino acid metabolism, and energy production via the oxidation of inorganic sulfur compounds. Transcriptomic analysis indicated that 28.4% of genes were regulated by carbon concentration, with increased carbon concentration inducing the expression of key enzymes in the EMP, ED, PP, and TCA cycles, genes responsible for the transformation of amino acids into TCA intermediates, as well as the sox genes for thiosulfate oxidation. Metabolomics showed that amino acid metabolism was enhanced and preferred in the presence of a high carbon concentration. Mutation of the sox genes decreased cell proton motive force when grown with amino acids and thiosulfate. In conclusion, we propose that copiotrophy in this Roseobacteraceae bacterium can be supported by amino acid metabolism and thiosulfate oxidation.

Specific plasticity of the anemone Anthopleura hermaphroditica to intertidal and subtidal environmental conditions of the Quempillén estuary

The cellular capacity of marine organisms to address rapid fluctuations in environmental conditions is decisive, especially when their bathymetric distribution encompasses intertidal and subtidal zones of estuarine systems. To understand how the bathymetric distribution determines the oxidative damage and antioxidant response of the estuarine anemone Anthopleura hermaphroditica, individuals were collected from upper intertidal and shallow subtidal zones of Quempillén River estuary (Chile), and their response analysed in a fully orthogonal, multifactorial laboratory experiment. The organisms were exposed to the effects of temperature (10°C and 30°C), salinity (10 ppt and 30 ppt) and radiation (PAR, > 400-700 nm; PAR+UV-A, > 320-700 nm; PAR+UV-A+UV-B, > 280-700 nm), and their levels of lipid peroxidation, protein carbonyl and total antioxidant capacity were determined. The results indicated that the intertidal individuals of A. hermaphroditica presented higher levels of tolerance to the stressful ranges of temperature, salinity, and radiation than individuals from the subtidal zone, which was evident from their lower levels of oxidative damage to lipids and proteins. These results were consistent with increased levels of total antioxidant capacity observed in subtidal organisms. Thus intertidal individuals could have greater plasticity to environmental variations than subtidal individuals. Future studies are needed to understand the mechanisms underlying stress adaptation in individuals from this estuarine anemone subjected to different environmental stressors during their life cycles.

Microbial Richness of Marine Biofilms Revealed by Sequencing Full-Length 16S rRNA Genes

Marine biofilms are a collective of microbes that can grow on many different surfaces immersed in marine environments. Estimating the microbial richness and specificity of a marine biofilm community is a challenging task due to the high complexity in comparison with seawater. Here, we compared the resolution of full-length 16S rRNA gene sequencing technique of a PacBio platform for microbe identification in marine biofilms with the results of partial 16S rRNA gene sequencing of traditional Illumina PE250 platform. At the same time, the microbial richness, diversity, and composition of adjacent seawater communities in the same batch of samples were analyzed. Both techniques revealed higher species richness, as reflected by the Chao1 index, in the biofilms than that in the seawater communities. Moreover, compared with Illumina sequencing, PacBio sequencing detected more specific species for biofilms and less specific species for seawater. Members of Vibrio, Arcobacter, Photobacterium, Pseudoalteromonas, and Thalassomonas were significantly enriched in the biofilms, which is consistent with the previous understanding of species adapted to a surface-associated lifestyle and validates the taxonomic analyses in the current study. To conclude, the full-length sequencing of 16S rRNA genes has probably a stronger ability to analyze more complex microbial communities, such as marine biofilms, the species richness of which has probably been under-estimated in previous studies.

Role of intertidal microbial communities in carbon dioxide sequestration and pollutant removal: A review

Intertidal microbial communities occur as biofilms or microphytobenthos (MPB) which are sediment-attached assemblages of bacteria, protozoa, fungi, algae, diatoms embedded in extracellular polymeric substances. Despite their global occurrence, they have not been reviewed in light of their structural and functional characteristics. This paper reviews the importance of such microbial communities and their importance in carbon dioxide sequestration as well as pollutant bioremediation. Global annual benthic microalgal productivity was 500 million tons of carbon, 50% of which contributed towards the autochthonous carbon fixation in the estuaries. Primary production by MPB was 27-234 gCm^-2y^-1 in the estuaries of Asia, Europe and the United States. Mechanisms of heavy metal removal remain to be tested in intertidal communities. Cyanobacteria facilitate hydrocarbon degradation in intertidal biofilms and microbial mats by supporting the associated sulfate-reducing bacteria and aerobic heterotrophs. Physiological cooperation between the microorganisms in intertidal communities imparts enhanced ability to utilize polycyclic aromatic hydrocarbon pollutants by these microorganisms than mono-species communities. Future research may be focused on biochemical characteristics of intertidal mats and biofilms, pollutant-microbial interactions and ecosystem influences.

Metagenomic analysis reveals genetic insights on biogeochemical cycling, xenobiotic degradation, and stress resistance in mudflat microbiome

Mudflats are highly productive coastal ecosystems that are dominated by halophytic vegetation. In this study, the mudflat sediment microbiome was investigated from Nalabana Island, located in a brackish water coastal wetland of India; Chilika, based on the MinION shotgun metagenomic analysis. Bacterial, archaeal, and fungal communities were mostly composed of Proteobacteria (38.3%), Actinobacteria (20.7%), Euryarchaeota (76.1%), Candidatus Bathyarchaeota (6.8%), Ascomycota (47.2%), and Basidiomycota (22.0%). Bacterial and archaeal community composition differed significantly between vegetated mudflat and un-vegetated bulk sediments. Carbon, nitrogen, sulfur metabolisms, oxidative phosphorylation, and xenobiotic biodegradation were the most common microbial functionalities in the mudflat metagenomes. Furthermore, genes involved in oxidative stresses, osmotolerance, secondary metabolite synthesis, and extracellular polymeric substance synthesis revealed adaptive mechanisms of the microbiome in mudflat habitat. Mudflat metagenome also revealed genes involved in the plant growth and development, suggesting that microbial communities could aid halophytic vegetation by providing tolerance to the abiotic stresses in a harsh mudflat environment. Canonical correspondence analysis and co-occurrence network revealed that both biotic (vegetation and microbial interactions) and abiotic factors played important role in shaping the mudflat microbiome composition. Among abiotic factors, pH accounted for the highest variance (20.10%) followed by available phosphorus (19.73%), total organic carbon (9.94%), salinity (8.28%), sediment texture (sand) (6.37%) and available nitrogen (5.53%) in the mudflat microbial communities. Overall, this first metagenomic study provided a comprehensive insight on the community structure, potential ecological interactions, and genetic potential of the mudflat microbiome in context to the cycling of organic matter, xenobiotic biodegradation, stress resistance, and in providing the ecological fitness to halophytes. These ecosystem services of the mudflat microbiome must be considered in the conservation and management plan of coastal wetlands. This study also advanced our understanding of fungal diversity which is understudied from the coastal lagoon ecosystems.

Analysis of Bacterial Communities on North Sea Macroalgae and Characterization of the Isolated Planctomycetes Adhaeretor mobilis gen. nov., sp. nov., Roseimaritima multifibrata sp. nov., Rosistilla ulvae sp. nov. and Rubripirellula lacrimiformis sp. nov

Planctomycetes are bacteria that were long thought to be unculturable, of low abundance, and therefore neglectable in the environment. This view changed in recent years, after it was shown that members of the phylum Planctomycetes can be abundant in many aquatic environments, e.g., in the epiphytic communities on macroalgae surfaces. Here, we analyzed three different macroalgae from the North Sea and show that Planctomycetes is the most abundant bacterial phylum on the alga Fucus sp., while it represents a minor fraction of the surface-associated bacterial community of Ulva sp. and Laminaria sp. Especially dominant within the phylum Planctomycetes were Blastopirellula sp., followed by Rhodopirellula sp., Rubripirellula sp., as well as other Pirellulaceae and Lacipirellulaceae, but also members of the OM190 lineage. Motivated by the observed abundance, we isolated four novel planctomycetal strains to expand the collection of species available as axenic cultures since access to different strains is a prerequisite to investigate the success of planctomycetes in marine environments. The isolated strains constitute four novel species belonging to one novel and three previously described genera in the order Pirellulales, class Planctomycetia, phylum Planctomycetes.

The Microbiome of Posidonia oceanica Seagrass Leaves Can Be Dominated by Planctomycetes

Seagrass meadows are ubiquitous, fragile and endangered marine habitats, which serve as fish breeding grounds, stabilize ocean floor substrates, retain nutrients and serve as important carbon sinks, counteracting climate change. In the Mediterranean Sea, seagrass meadows are mostly formed by the slow-growing endemic plant Posidonia oceanica (Neptune grass), which is endangered by global warming and recreational motorboating. Despite its importance, surprisingly little is known about the leaf surface microbiome of P. oceanica. Using amplicon sequencing, we here show that species belonging to the phylum Planctomycetes can dominate the biofilms of young and aged P. oceanica leaves. Application of selective cultivation techniques allowed for the isolation of two novel planctomycetal strains belonging to two yet uncharacterized genera.

Tissue-specific localization of polyketide synthase and other associated genes in the lichen, Cladonia rangiferina, using laser microdissection

The biosynthesis of two polyketides, atranorin and fumarprotocetraric acid, produced from a lichen-forming fungus, Cladonia rangiferina (L.) F. H. Wigg. was correlated with the expression of eight fungal genes (CrPKS1, CrPKS3, CrPKS16, Catalase (CAT), Sugar Transporter (MFsug), Dioxygenase (YQE1), C2H2 Transcription factor (C2H2), Transcription Factor PacC (PacC), which are thought to be involved in polyketide biosynthesis, and one algal gene, NAD-dependent deacetylase sirtuin 2 (AsNAD)), using laser microdissection (LMD). The differential gene expression levels within the thallus tissue layers demonstrate that the most active region for potential polyketide biosynthesis within the lichen is the outer apical region proximal to the photobiont but some expression also occurs in reproductive tissue. This is the first study using laser microdissection to explore gene expression of these nine genes and their location of expression; it provides a proof-of-concept for future experiments exploring tissue-specific gene expression within lichens; and it highlights the utility of LMD for use in lichen systems.

Genomic and Transcriptomic Evidence for Carbohydrate Consumption among Microorganisms in a Cold Seep Brine Pool

The detailed lifestyle of microorganisms in deep-sea brine environments remains largely unexplored. Using a carefully calibrated genome binning approach, we reconstructed partial to nearly-complete genomes of 51 microorganisms in biofilms from the Thuwal cold seep brine pool of the Red Sea. The recovered metagenome-assembled genomes (MAGs) belong to six different phyla: Actinobacteria, Proteobacteria, Candidatus Cloacimonetes, Candidatus Marinimicrobia, Bathyarchaeota, and Thaumarchaeota. By comparison with close relatives of these microorganisms, we identified a number of unique genes associated with organic carbon metabolism and energy generation. These genes included various glycoside hydrolases, nitrate and sulfate reductases, putative bacterial microcompartment biosynthetic clusters (BMC), and F₄₂₀H₂ dehydrogenases. Phylogenetic analysis suggested that the acquisition of these genes probably occurred through horizontal gene transfer (HGT). Metatranscriptomics illustrated that glycoside hydrolases are among the most highly expressed genes. Our results suggest that the microbial inhabitants are well adapted to this brine environment, and anaerobic carbohydrate consumption mediated by glycoside hydrolases and electron transport systems (ETSs) is a dominant process performed by microorganisms from various phyla within this ecosystem.

Deciphering the recent phylogenetic expansion of the originally deeply rooted Mycobacterium tuberculosis lineage 7

Background

A deeply rooted phylogenetic lineage of Mycobacterium tuberculosis (M. tuberculosis) termed lineage 7 was discovered in Ethiopia. Whole genome sequencing of 30 lineage 7 strains from patients in Ethiopia was performed. Intra-lineage genome variation was defined and unique characteristics identified with a focus on genes involved in DNA repair, recombination and replication (3R genes).

Results

More than 800 mutations specific to M. tuberculosis lineage 7 strains were identified. The proportion of non-synonymous single nucleotide polymorphisms (nsSNPs) in 3R genes was higher after the recent expansion of M. tuberculosis lineage 7 strain started. The proportion of nsSNPs in genes involved in inorganic ion transport and metabolism was significantly higher before the expansion began. A total of 22346 bp deletions were observed. Lineage 7 strains also exhibited a high number of mutations in genes involved in carbohydrate transport and metabolism, transcription, energy production and conversion.

Conclusions

We have identified unique genomic signatures of the lineage 7 strains. The high frequency of nsSNP in 3R genes after the phylogenetic expansion may have contributed to recent variability and adaptation. The abundance of mutations in genes involved in inorganic ion transport and metabolism before the expansion period may indicate an adaptive response of lineage 7 strains to enable survival, potentially under environmental stress exposure. As lineage 7 strains originally were phylogenetically deeply rooted, this may indicate fundamental adaptive genomic pathways affecting the fitness of M. tuberculosis as a species.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0715-z) contains supplementary material, which is available to authorized users.

Intraspecific Variation in Microbial Symbiont Communities of the Sun Sponge, Hymeniacidon heliophila, from Intertidal and Subtidal Habitats

Sponges host diverse and complex communities of microbial symbionts that display a high degree of host specificity. The microbiomes of conspecific sponges are relatively constant, even across distant locations, yet few studies have directly examined the influence of abiotic factors on intraspecific variation in sponge microbial community structure. The contrast between intertidal and subtidal environments is an ideal system to assess the effect of environmental variation on sponge-microbe symbioses, producing two drastically different environments on a small spatial scale. Here, we characterized the microbial communities of individual intertidal and subtidal Hymeniacidon heliophila sponges, ambient seawater, and sediment from a North Carolina oyster reef habitat by partial (Illumina sequencing) and nearly full-length (clone libraries) 16S rRNA gene sequence analyses. Clone library sequences were compared to H. heliophila symbiont communities from the Gulf of Mexico and Brazil, revealing strong host specificity of dominant symbiont taxa across expansive geographic distances. Sediment and seawater samples yielded clearly distinct microbial communities from those found in H. heliophila. Despite the close proximity of the sponges sampled, significant differences between subtidal and intertidal sponges in the diversity, structure, and composition of their microbial communities were detected. Differences were driven by changes in the relative abundance of a few dominant microbial symbiont taxa, as well as the presence or absence of numerous rare microbial taxa. These findings suggest that extreme abiotic fluctuations, such as periodic air exposure in intertidal habitats, can drive intraspecific differences in complex host-microbe symbioses.

Changing composition of microbial communities indicates seepage fluid difference of the Thuwal Seeps in the Red Sea

Cold seeps are unique ecosystems that are generally characterized by high salinity and reducing solutions. Seepage fluid, the major water influx of this system, contains hypersaline water, sediment pore water, and other components. The Thuwal cold seeps were recently discovered on the continental margin of the Red Sea. Using 16S rRNA gene pyro-sequencing technology, microbial communities were investigated by comparing samples collected in 2011 and 2013. The results revealed differences in the microbial communities between the two sampling times. In particular, a significantly higher abundance of Marine Group I (MGI) Thaumarchaeota was coupled with lower salinity in 2013. In the brine pool, the dominance of Desulfobacterales in 2011 was supplanted by MGI Thaumarchaeota in 2013, perhaps due to a reduced supply of hydrogen sulfide from the seepage fluid. Collectively, this study revealed a difference in water components in this ecosystem between two sampling times. The results indicated that the seawater in this cold seep displayed a greater number of characteristics of normal seawater in 2013 than in 2011, which might represent the dominant driving force for changes in microbial community structures. This is the first study to provide a temporal comparison of the microbial biodiversity of a cold seep ecosystem in the Red Sea.

Extracellular matrix-associated proteins form an integral and dynamic system during Pseudomonas aeruginosa biofilm development

Though the essential role of extracellular matrix in biofilm development has been extensively documented, the function of matrix-associated proteins is elusive. Determining the dynamics of matrix-associated proteins would be a useful way to reveal their functions in biofilm development. Therefore, we applied iTRAQ-based quantitative proteomics to evaluate matrix-associated proteins isolated from different phases of Pseudomonas aeruginosa ATCC27853 biofilms. Among the identified 389 proteins, 54 changed their abundance significantly. The increased abundance of stress resistance and nutrient metabolism-related proteins over the period of biofilm development was consistent with the hypothesis that biofilm matrix forms micro-environments in which cells are optimally organized to resist stress and use available nutrients. Secreted proteins, including novel putative effectors of the type III secretion system were identified, suggesting that the dynamics of pathogenesis-related proteins in the matrix are associated with biofilm development. Interestingly, there was a good correlation between the abundance changes of matrix-associated proteins and their expression. Further analysis revealed complex interactions among these modulated proteins, and the mutation of selected proteins attenuated biofilm development. Collectively, this work presents the first dynamic picture of matrix-associated proteins during biofilm development, and provides evidences that the matrix-associated proteins may form an integral and well regulated system that contributes to stress resistance, nutrient acquisition, pathogenesis and the stability of the biofilm.

Seeing the forest for the genes: using metagenomics to infer the aggregated traits of microbial communities

Most environments harbor large numbers of microbial taxa with ecologies that remain poorly described and characterizing the functional capabilities of whole communities remains a key challenge in microbial ecology. Shotgun metagenomic analyses are increasingly recognized as a powerful tool to understand community-level attributes. However, much of this data is under-utilized due, in part, to a lack of conceptual strategies for linking the metagenomic data to the most relevant community-level characteristics. Microbial ecologists could benefit by borrowing the concept of community-aggregated traits (CATs) from plant ecologists to glean more insight from the ever-increasing amount of metagenomic data being generated. CATs can be used to quantify the mean and variance of functional traits found in a given community. A CAT-based strategy will often yield far more useful information for predicting the functional attributes of diverse microbial communities and changes in those attributes than the more commonly used analytical strategies. A more careful consideration of what CATs to measure and how they can be quantified from metagenomic data, will help build a more integrated understanding of complex microbial communities.

Species sorting during biofilm assembly by artificial substrates deployed in a cold seep system

Studies focusing on biofilm assembly in deep-sea environments are rarely conducted. To examine the effects of substrate type on microbial community assembly, biofilms were developed on different substrates for different durations at two locations in the Red Sea: in a brine pool and in nearby bottom water (NBW) adjacent to the Thuwal cold seep II. The composition of the microbial communities in 51 biofilms and water samples were revealed by classification of pyrosequenced 16S rRNA gene amplicons. Together with the microscopic characteristics of the biofilms, the results indicate a stronger selection effect by the substrates on the microbial assembly in the brine pool compared with the NBW. Moreover, the selection effect by substrate type was stronger in the early stages compared with the later stages of the biofilm development. These results are consistent with the hypotheses proposed in the framework of species sorting theory, which states that the power of species sorting during microbial community assembly is dictated by habitat conditions, duration and the structure of the source community. Therefore, the results of this study shed light on the control strategy underlying biofilm-associated marine fouling and provide supporting evidence for ecological theories important for understanding the formation of deep-sea biofilms.

In situ environment rather than substrate type dictates microbial community structure of biofilms in a cold seep system

Using microscopic and molecular techniques combined with computational analysis, this study examined the structure and composition of microbial communities in biofilms that formed on different artificial substrates in a brine pool and on a seep vent of a cold seep in the Red Sea to test our hypothesis that initiation of the biofilm formation and spreading mode of microbial structures differs between the cold seep and the other aquatic environments. Biofilms on different substrates at two deployment sites differed morphologically, with the vent biofilms having higher microbial abundance and better structural features than the pool biofilms. Microbes in the pool biofilms were more taxonomically diverse and mainly composed of various sulfate-reducing bacteria whereas the vent biofilms were exclusively dominated by sulfur-oxidizing Thiomicrospira. These results suggest that the redox environments at the deployment sites might have exerted a strong selection on microbes in the biofilms at two sites whereas the types of substrates had limited effects on the biofilm development.