CPR and DPANN Have an Overlooked Role in Corals' Microbial Community Structure.

Understanding how microbial communities are structured in coral holobionts is important to estimate local and global impacts and provide efficient environment management strategies. Several studies investigated the relationship between corals and their microbial communities, including the environmental drivers of shifts in this relationship, associated with diseases and coral cover loss. However, these studies are often geographically or taxonomically restricted and usually focused on the most abundant microbial groups, neglecting the rare biosphere, including archaea in the group DPANN and the recently discovered bacterial members of the candidate phyla radiation (CPR). Although it is known that rare microbes can play essential roles in several environments, we still lack understanding about which taxa comprise the rare biosphere of corals' microbiome. Here, we investigated the host-related and technical factors influencing coral microbial community structure and the importance of CPR and DPANN in this context by analyzing more than a hundred coral metagenomes from independent studies worldwide. We show that coral genera are the main biotic factor shaping coral microbial communities. We also detected several CPR and DPANN phyla comprising corals' rare biosphere for the first time and showed that they significantly contribute to shaping coral microbial communities.

Microbial community diversity and physical-chemical features of the Southwestern Atlantic Ocean.

Microbial oceanography studies have demonstrated the central role of microbes in functioning and nutrient cycling of the global ocean. Most of these former studies including at Southwestern Atlantic Ocean (SAO) focused on surface seawater and benthic organisms (e.g., coral reefs and sponges). This is the first metagenomic study of the SAO. The SAO harbors a great microbial diversity and marine life (e.g., coral reefs and rhodolith beds). The aim of this study was to characterize the microbial community diversity of the SAO along the depth continuum and different water masses by means of metagenomic, physical-chemical and biological analyses. The microbial community abundance and diversity appear to be strongly influenced by the temperature, dissolved organic carbon, and depth, and three groups were defined [1. surface waters; 2. sub-superficial chlorophyll maximum (SCM) (48-82 m) and 3. deep waters (236-1,200 m)] according to the microbial composition. The microbial communities of deep water masses [South Atlantic Central water, Antarctic Intermediate water and Upper Circumpolar Deep water] are highly similar. Of the 421,418 predicted genes for SAO metagenomes, 36.7 % had no homologous hits against 17,451,486 sequences from the North Atlantic, South Atlantic, North Pacific, South Pacific and Indian Oceans. From these unique genes from the SAO, only 6.64 % had hits against the NCBI non-redundant protein database. SAO microbial communities share genes with the global ocean in at least 70 cellular functions; however, more than a third of predicted SAO genes represent a unique gene pool in global ocean. This study was the first attempt to characterize the taxonomic and functional community diversity of different water masses at SAO and compare it with the microbial community diversity of the global ocean, and SAO had a significant portion of endemic gene diversity. Microbial communities of deep water masses (236-1,200 m) are highly similar, suggesting that these water masses have very similar microbiological attributes, despite the common knowledge that water masses determine prokaryotic community and are barriers to microbial dispersal. The present study also shows that SCM is a clearly differentiated layer within Tropical waters with higher abundance of phototrophic microbes and microbial diversity.

Gut microbiome signature and nasal lavage inflammatory markers in young people with asthma.

Background: Asthma is a complex disease and a severe global public health problem resulting from interactions between genetic background and environmental exposures. It has been suggested that gut microbiota may be related to asthma development; however, such relationships needs further investigation. Objective: This study aimed to characterize the gut microbiota as well as the nasal lavage cytokine profile of asthmatic and nonasthmatic individuals. Methods: Stool and nasal lavage samples were collected from 29 children and adolescents with type 2 asthma and 28 children without asthma in Brazil. Amplicon sequencing of the stool bacterial V4 region of the 16S rRNA gene was performed using Illumina MiSeq. Microbiota analysis was performed by QIIME 2 and PICRUSt2. Type 2 asthma phenotype was characterized by high sputum eosinophil counts and positive skin prick tests for house dust mite, cockroach, and/or cat or dog dander. The nasal immune marker profile was assessed using a customized multiplex panel. Results: Stool microbiota differed significantly between asthmatic and nonasthmatic participants (P = .001). Bacteroides was more abundant in participants with asthma (P < .05), while Prevotella was more abundant in nonasthmatic individuals (P < .05). In people with asthma, the relative abundance of Bacteroides correlated with IL-4 concentration in nasal lavage samples. Inference of microbiota functional capacity identified differential fatty acid biosynthesis in asthmatic compared to nonasthmatic subjects. Conclusion: The stool microbiota differed between asthmatic and nonasthmatic young people in Brazil. Asthma was associated with higher Bacteroides levels, which correlated with nasal IL-4 concentration.

Urbanization drives adaptive evolution in a Neotropical bird.

Urbanization has dramatic impacts on natural habitats and such changes may potentially drive local adaptation of urban populations. Behavioral change has been specifically shown to facilitate the fast adaptation of birds to changing environments, but few studies have investigated the genetic mechanisms of this process. Such investigations could provide insights into questions about both evolutionary theory and management of urban populations. In this study, we investigated whether local adaptation has occurred in urban populations of a Neotropical bird species, Coereba flaveola, specifically addressing whether observed behavioral adaptations are correlated to genetic signatures of natural selection. To answer this question, we sampled 24 individuals in urban and rural environments, and searched for selected loci through a genome-scan approach based on RADseq genomic data, generated and assembled using a reference genome for the species. We recovered 46 loci as putative selection outliers, and 30 of them were identified as associated with biological processes possibly related to urban adaptation, such as the regulation of energetic metabolism, regulation of genetic expression, and changes in the immunological system. Moreover, genes involved in the development of the nervous system showed signatures of selection, suggesting a link between behavioral and genetic adaptations. Our findings, in conjunction with similar results in previous studies, support the idea that cities provide a similar selective pressure on urban populations and that behavioral plasticity may be enhanced through genetic changes in urban populations.

Ecological landscape explains aquifers microbial structure.

Aquifers have significant social, economic, and ecological importance. They supply 30 % of the freshwater for human consumption worldwide, including agricultural and industrial use. Despite aquifers' importance, the relationships between aquifer categories and their inhabiting microbial communities are still unknown. Characterizing variations within microbial communities' function and taxonomy structure at different aquifers could give a panoramic view of patterns that may enable the detection and prediction of environmental impact caused by multiple sources. Using publicly available shotgun metagenomic datasets, we examined whether soil properties, land use, and climate variables would have a more significant influence on the taxonomy and functional structure of the microbial communities than the ecological landscapes of the aquifer (i.e., Karst, Porous, Saline, Geyser, and Porous Contaminated). We found that these categories are stronger predictors of microbial communities' structure than geographical localization. In addition, our results show that microbial richness and dominance patterns are the opposite of those found in multicellular life, where extreme habitats harbour richer functional and taxonomic microbial communities. We found that low-abundant and recently described candidate taxa, such as the chemolithoautotrophic genus Candidatus Altiarcheum and the Candidate phylum Parcubacteria, are the main contributors to aquifer microbial communities' dissimilarities. Genes related to gram-negative bacteria proteins, cell wall structures, and phage activity were the primary contributors to aquifer microbial communities' dissimilarities among the aquifers' ecological landscapes. The results reported in the present study highlight the utility of using ecological landscapes for investigating aquifer microbial communities. In addition, we suggest that functions played by recently described and low abundant bacterial groups need further investigation once they might affect water quality, geochemical cycles, and the effects of anthropogenic disturbances such as pollution and climatic events on aquifers.

Mangrove microbial community recovery and their role in early stages of forest recolonization within shrimp ponds.

Shrimp farming is blooming worldwide, posing a severe threat to mangroves and its multiple goods and ecosystem services. Several studies reported the impacts of aquaculture on mangrove biotic communities, including microbiomes. However, little is known about how mangrove soil microbiomes would change in response to mangrove forest recolonization. Using genome-resolved metagenomics, we compared the soil microbiome of mangrove forests (both with and without the direct influence of shrimp farming effluents) with active shrimp farms and mangroves under a recolonization process. We found that the structure and composition of active shrimp farms microbial communities differ from the control mangrove forests, mangroves under the impact of the shrimp farming effluents, and mangroves under recolonization. Shrimp farming ponds microbiomes have lower microbial diversity and are dominated by halophilic microorganisms, presenting high abundance of multiple antibiotic resistance genes. On the other hand, control mangrove forests, impacted mangroves (exposed to the shrimp farming effluents), and recolonization ponds were more diverse, with a higher abundance of genes related to carbon mobilization. Our data also indicated that the microbiome is recovering in the mangrove recolonization ponds, performing vital metabolic functions and functionally resembling microbiomes found in those soils of neighboring control mangrove forests. Despite highlighting the damage caused by the habitat changes in mangrove soil microbiome community and functioning, our study sheds light on these systems incredible recovery capacity. Our study shows the importance of natural mangrove forest recovery, enhancing ecosystem services by the soil microbial communities even in a very early development stage of mangrove forest, thus encouraging mangrove conservation and restoration efforts worldwide.

Understanding Asthma and Allergies by the Lens of Biodiversity and Epigenetic Changes.

Exposure to different organisms (bacteria, mold, virus, protozoan, helminths, among others) can induce epigenetic changes affecting the modulation of immune responses and consequently increasing the susceptibility to inflammatory diseases. Epigenomic regulatory features are highly affected during embryonic development and are responsible for the expression or repression of different genes associated with cell development and targeting/conducting immune responses. The well-known, "window of opportunity" that includes maternal and post-natal environmental exposures, which include maternal infections, microbiota, diet, drugs, and pollutant exposures are of fundamental importance to immune modulation and these events are almost always accompanied by epigenetic changes. Recently, it has been shown that these alterations could be involved in both risk and protection of allergic diseases through mechanisms, such as DNA methylation and histone modifications, which can enhance Th2 responses and maintain memory Th2 cells or decrease Treg cells differentiation. In addition, epigenetic changes may differ according to the microbial agent involved and may even influence different asthma or allergy phenotypes. In this review, we discuss how exposure to different organisms, including bacteria, viruses, and helminths can lead to epigenetic modulations and how this correlates with allergic diseases considering different genetic backgrounds of several ancestral populations.

Repeated selective enrichment process of sediment microbiota occurred in sea cucumber guts.

Deposit-feeding sea cucumbers repeat ingestion of sediments and excretion of faeces daily and consequently increase bacterial abundance in sediments and promote organic matter mineralization. Such ecological roles are expected to be collaborative activities of sea cucumbers and the gut microbiota. Here, we performed a spatiotemporally broad 16S rRNA gene analysis using 109 samples from sea cucumber faeces and habitat sediments to explore potential contribution of their gut microbiota to the ecological roles. Most operational taxonomic units (OTUs) observed in the faecal samples were shared with the sediment samples, nevertheless faecal and sediment microbiota differed from each other in UniFrac analysis. Lower bacterial diversity and increased relative abundance of specific OTUs in the faecal microbiota strongly suggest selective enrichment of ingested sediment microbiota in their guts. Interestingly, representative faecal OTUs were more abundant in sea cucumber-populated sediments than in un-inhabited sediments, indicating bacteria selectively enriched in the guts were spread on ambient sediments via faeces. Moreover, the predicted microbial community metabolic potential showed a higher abundance of genes related to carbohydrate and xenobiotics metabolisms in faeces than in sediments. Our study suggests the repeated selective enrichment transforms ambient sediment microbial communities and maintains the host's ecological roles by promoting organic matter mineralization.

Integrating Computational Methods to Investigate the Macroecology of Microbiomes.

Studies in microbiology have long been mostly restricted to small spatial scales. However, recent technological advances, such as new sequencing methodologies, have ushered an era of large-scale sequencing of environmental DNA data from multiple biomes worldwide. These global datasets can now be used to explore long standing questions of microbial ecology. New methodological approaches and concepts are being developed to study such large-scale patterns in microbial communities, resulting in new perspectives that represent a significant advances for both microbiology and macroecology. Here, we identify and review important conceptual, computational, and methodological challenges and opportunities in microbial macroecology. Specifically, we discuss the challenges of handling and analyzing large amounts of microbiome data to understand taxa distribution and co-occurrence patterns. We also discuss approaches for modeling microbial communities based on environmental data, including information on biological interactions to make full use of available Big Data. Finally, we summarize the methods presented in a general approach aimed to aid microbiologists in addressing fundamental questions in microbial macroecology, including classical propositions (such as "everything is everywhere, but the environment selects") as well as applied ecological problems, such as those posed by human induced global environmental changes.

Metagenomics of Coral Reefs Under Phase Shift and High Hydrodynamics.

Local and global stressors have affected coral reef ecosystems worldwide. Switches from coral to algal dominance states and microbialization are the major processes underlying the global decline of coral reefs. However, most of the knowledge concerning microbialization has not considered physical disturbances (e.g., typhoons, waves, and currents). Southern Japan reef systems have developed under extreme physical disturbances. Here, we present analyses of a three-year investigation on the coral reefs of Ishigaki Island that comprised benthic and fish surveys, water quality analyses, metagenomics and microbial abundance data. At the four studied sites, inorganic nutrient concentrations were high and exceeded eutrophication thresholds. The dissolved organic carbon (DOC) concentration (up to 233.3 µM) and microbial abundance (up to 2.5 × 105 cell/mL) values were relatively high. The highest vibrio counts coincided with the highest turf cover (∼55-85%) and the lowest coral cover (∼4.4-10.2%) and fish biomass (0.06 individuals/m2). Microbiome compositions were similar among all sites and were dominated by heterotrophs. Our data suggest that a synergic effect among several regional stressors are driving coral decline. In a high hydrodynamics reef environment, high algal/turf cover, stimulated by eutrophication and low fish abundance due to overfishing, promote microbialization. Together with crown-of-thorns starfish (COTS) outbreaks and possible of climate changes impacts, theses coral reefs are likely to collapse.

Molecular Mechanisms for Microbe Recognition and Defense by the Red Seaweed Laurencia dendroidea.

The ability to recognize and respond to the presence of microbes is an essential strategy for seaweeds to survive in the marine environment, but understanding of molecular seaweed-microbe interactions is limited. Laurencia dendroidea clones were inoculated with the marine bacterium Vibrio madracius. The seaweed RNA was sequenced, providing an unprecedentedly high coverage of the transcriptome of Laurencia, and the gene expression levels were compared between control and inoculated samples after 24, 48, and 72 h. Transcriptomic changes in L. dendroidea in the presence of V. madracius include the upregulation of genes that participate in signaling pathways described here for the first time as a response of seaweeds to microbes. Genes coding for defense-related transcription activators, reactive oxygen species metabolism, terpene biosynthesis, and energy conversion pathways were upregulated in inoculated samples of L. dendroidea, indicating an integrated defensive system in seaweeds. This report contributes significantly to the current knowledge about the molecular mechanisms involved in the highly dynamic seaweed-bacterium interactions. IMPORTANCE Marine bacteria are part of the healthy microbiota associated with seaweeds, but some species, such as Vibrio spp., are frequently associated with disease outbreaks, especially in economically valuable cultures. In this context, the ability of seaweeds to recognize microbes and, when necessary, activate defense mechanisms is essential for their survival. However, studies dedicated to understanding the molecular components of the immune response in seaweeds are rare and restricted to indirect stimulus. This work provides an unprecedentedly large-scale evaluation of the transcriptional changes involved in microbe recognition, cellular signaling, and defense in the red seaweed Laurencia dendroidea in response to the marine bacterium Vibrio madracius. By expanding knowledge about seaweed-bacterium interactions and about the integrated defensive system in seaweeds, this work offers the basis for the development of tools to increase the resistance of cultured seaweeds to bacterial infections.

Individual Apostichopus japonicus fecal microbiome reveals a link with polyhydroxybutyrate producers in host growth gaps.

Gut microbiome shapes various aspects of a host's physiology, but these functions in aquatic animal hosts have yet to be fully investigated. The sea cucumber Apostichopus japonicus Selenka is one such example. The large growth gap in their body size has delayed the development of intensive aquaculture, nevertheless the species is in urgent need of conservation. To understand possible contributions of the gut microbiome to its host's growth, individual fecal microbiome comparisons were performed. High-throughput 16S rRNA sequencing revealed significantly different microbiota in larger and smaller individuals; Rhodobacterales in particular was the most significantly abundant bacterial group in the larger specimens. Further shotgun metagenome of representative samples revealed a significant abundance of microbiome retaining polyhydroxybutyrate (PHB) metabolism genes in the largest individual. The PHB metabolism reads were potentially derived from Rhodobacterales. These results imply a possible link between microbial PHB producers and potential growth promotion in Deuterostomia marine invertebrates.

Vibrio ishigakensis sp. nov., in Halioticoli clade isolated from seawater in Okinawa coral reef area, Japan.

Five novel strains showing non-motile, alginolytic, halophilic and fermentative features were isolated from seawater samples off Okinawa in coral reef areas. These strains were characterized by an advanced polyphasic taxonomy including genome based taxonomy using multilocus sequence analysis (MLSA) and in silico DNA-DNA similarity (in silico DDH). Phylogenetic analyses on the basis of 16S rRNA gene sequences revealed that the isolates could be assigned to the genus Vibrio, however they were not allocated into any distinct cluster with known Vibrionaceae species. MLSA based on eight protein-coding genes (gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA) showed the vibrios formed an outskirt branch of Halioticoli clade. The experimental DNA-DNA hybridization data revealed that the five strains were in the range of being defined as conspecific but separate from nine Halioticoli clade species. The G+C contents of the Vibrio ishigakensis strains were 47.3-49.1mol%. Both Amino Acid Identity and Average Nucleotide Identity of the strain C1(T) against Vibrio ezurae HDS1-1(T), Vibrio gallicus HT2-1(T), Vibrio halioticoli IAM 14596(T), Vibrio neonatus HDD3-1(T) and Vibrio superstes G3-29(T) showed less than 95% similarity. The genome-based taxonomic approach by means of in silico DDH values also supports the V. ishigakensis strains being distinct from the other known Halioticoli clade species. Sixteen traits (growth temperature range, DNase and lipase production, indole production, and assimilation of 10 carbon compounds) distinguished these strains from Halioticoli clade species. The names V. ishigakensis sp. nov. is proposed for the species of Halioticoli clade, with C1(T) as the type strain (JCM 19231(T)=LMG 28703(T)).

BaMBa: towards the integrated management of Brazilian marine environmental data.

A new open access database, Brazilian Marine Biodiversity (BaMBa) (https://marinebiodiversity.lncc.br), was developed in order to maintain large datasets from the Brazilian marine environment. Essentially, any environmental information can be added to BaMBa. Certified datasets obtained from integrated holistic studies, comprising physical-chemical parameters, -omics, microbiology, benthic and fish surveys can be deposited in the new database, enabling scientific, industrial and governmental policies and actions to be undertaken on marine resources. There is a significant number of databases, however BaMBa is the only integrated database resource both supported by a government initiative and exclusive for marine data. BaMBa is linked to the Information System on Brazilian Biodiversity (SiBBr, http://www.sibbr.gov.br/) and will offer opportunities for improved governance of marine resources and scientists' integration. Database URL: http://marinebiodiversity.lncc.br.

Draft Genome Sequences of Two Vibrionaceae Species, Vibrio ponticus C121 and Photobacterium aphoticum C119, Isolated as Coral Reef Microbiota.

Here, the draft genome sequences of two Vibrionaceae, Vibrio ponticus C121 and Photobacterium aphoticum C119, which were isolated from the coral reef vicinity in Okinawa, Japan, are reported. The genome provides further insight into the genomic plasticity, biocomplexity, and ecophysiology, including pathogenicity and evolution, of these genera.