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Climate change is enhancing the frequency of cyanobacterial blooms not only during summer but also in spring and autumn, leading to increased ecological impacts. The bacterioplankton community composition (BCC), in particular, is deeply affected by these blooms, although at the same time BCC can also play important roles in blooms’ dynamics. However, more information is still needed regarding BCC during species-specific cyanobacterial blooms. The goal of this study was to assess BCC succession in a hypereutrophic shallow lake (Vela Lake, Portugal) during a warm spring using a metagenomic approach to provide a glimpse of the changes these communities experience during the dominance of Aphanizomenon-like bloom-forming species. BCC shifts were studied using 16S rRNA gene metabarcoding and multivariate analyses. A total of 875 operational taxonomic units (OTUs) were retrieved from samples. In early spring, the dominant taxa belonged to Proteobacteria (mainly Alphaproteobacteria—Rickettsiales) and Bacteroidetes (Saprospirales, Flavobacteriales and Sphingobacteriales). However, at the end of May, a bloom co-dominated by cyanobacterial populations of Aphanizomenon gracile, Sphaerospermopsis aphanizomenoides and Synechococcus sp. developed and persisted until the end of spring. This led to a major BCC shift favouring the prevalence of Alphaproteobacteria (Rickettsiales and also Rhizobiales, Caulobacteriales and Rhodospirillales) and Bacteroidetes (Saprospirales, followed by Flavobacteriales and Sphingobacteriales). These results contribute to the knowledge of BCC dynamics during species-specific cyanobacterial blooms, showing that BCC is strongly affected (directly or indirectly) by Aphanizomenon-Sphaerospermopsis blooms., This work had the financial support from CESAM (UID/AMB/50017/2019), FCT/MCTES and FEDER (PT2020 Partnership Agreement and Compete 2020). FCT (Fundação para a Ciência e Tecnologia) funded a post-doc grant SFRH/BPD/74184/2010 and a research contract for D.R.d.F. supported by national funds (OE), according to the DL 57/2016. A.R.M.P. was supported by a postdoctoral scholarship (SFRH/BPD/117563/2016) funded by the Portuguese Foundation for Science and Technology (FCT)/national funds (MCTES) and by the European Social Fund (ESF)/EU.

Marine sponges are abundant and ecologically important components of coral reefs and have been shown to harbour exceptionally high microbial densities, which can differ substantially among sponge species. However, this dichotomy between high and low microbial abundance (HMA, LMA) sponges is still not fully understood, particularly as concerns the archaeal community. This study aims to fill this gap by analysing (using 454-pyrosequencing of the 16S rRNA gene) how the archaeal community varies among known LMA (Stylissa carteri, and Stylissa massa), known HMA (Hyrtios erectus and Xestospongia testudinaria) and unknown HMA/LMA status sponge species (Ectyoplasia coccinea, Paratetilla bacca and Petrosia aff. spheroida) collected in a remote location in which very few sponge microbial composition studies have been previously performed (Mayotte, Comores archipelago, France) and comparing the results with those reported in four other geographical areas. Based on archaeal community composition, the known LMA sponges formed a distinct cluster together with Paratetilla bacca, Ectyoplasia coccinea and seawater while the known HMA sponge X. testudinaria formed a cluster with Petrosia aff. spheroida. The known HMA sponge H. erectus, in turn, had an intermediate archaeal community between HMA sponges and sediment samples. In addition to the above, we also showed significant compositional congruence between archaeal and bacterial communities sampled from the same sponge individuals. HMA sponges were mainly dominated by members assigned to the genus Nitrosopumilus while LMA sponges were mainly dominated by members assigned to the genus Cenarchaeum. In general, there was no clear difference in richness between HMA and LMA sponges. Evenness, however, was higher in HMA than LMA sponges. Whilst the present study corroborates some of the traits commonly associated with the HMA-LMA dichotomy (higher evenness in Mayotte HMA sponges), this was not consistent across geographical areas showing that more research is needed to fully understand the HMA/LMA dichotomy as concerns Archaea.

Here, we report on the draft genome sequence of Vibrio mediterranei strain CyArs1, isolated from the marine sponge Cinachyrella sp. Genome annotation revealed multiple genomic features, including eukaryotic-like repeat protein- and multidrug resistance-encoding genes, potentially involved in symbiotic relationships with the sponge host.

Understanding the maintenance and origin of beta diversity is a central topic in ecology. However, the factors that drive diversity patterns and underlying processes remain unclear, particularly for host-prokaryotic associations. Here, beta diversity patterns were studied in five prokaryotic biotopes, namely, two high microbial abundance (HMA) sponge taxa (Xestospongia spp. and Hyrtios erectus), one low microbial abundance (LMA) sponge taxon (Stylissa carteri), sediment and seawater sampled across thousands of kilometres. Using multiple regression on distance matrices (MRM), spatial (geographic distance) and environmental (sea surface temperature and chlorophyll α concentrations) variables proved significant predictors of beta diversity in all five biotopes and together explained from 54% to 82% of variation in dissimilarity of both HMA species, 27% to 43% of variation in sediment and seawater, but only 20% of variation of the LMA S. carteri. Variance partitioning was subsequently used to partition the variation into purely spatial, purely environmental and spatially-structured environmental components. The amount of variation in dissimilarity explained by the purely spatial component was lowest for S. carteri at 11% and highest for H. erectus at 55%. The purely environmental component, in turn, only explained from 0.15% to 2.83% of variation in all biotopes. In addition to spatial and environmental variables, a matrix of genetic differences between pairs of sponge individuals also proved a significant predictor of variation in prokaryotic dissimilarity of the Xestospongia species complex. We discuss the implications of these results for the HMA-LMA dichotomy and compare the MRM results with results obtained using constrained ordination and zeta diversity.

Microbial communities associated with sponges play important roles in sponge health, defence and nutrient dynamics in coral reef systems. Here, we used a 16S rRNA gene high-throughput sequencing ap...

Disturbances alter biodiversity via their specific characteristics, including severity and extent in the landscape, which act at different temporal and spatial scales. Biodiversity response to disturbance also depends on the community characteristics and habitat requirements of species. Untangling the mechanistic interplay of these factors has guided disturbance ecology for decades, generating mixed scientific evidence of biodiversity responses to disturbance. Understanding the impact of natural disturbances on biodiversity is increasingly important due to human-induced changes in natural disturbance regimes. In many areas, major natural forest disturbances, such as wildfires, windstorms, and insect outbreaks, are becoming more frequent, intense, severe, and widespread due to climate change and land-use change. Conversely, the suppression of natural disturbances threatens disturbance-dependent biota. Using a meta-analytic approach, we analysed a global data set (with most sampling concentrated in temperate and boreal secondary forests) of species assemblages of 26 taxonomic groups, including plants, animals, and fungi collected from forests affected by wildfires, windstorms, and insect outbreaks. The overall effect of natural disturbances on α-diversity did not differ significantly from zero, but some taxonomic groups responded positively to disturbance, while others tended to respond negatively. Disturbance was beneficial for taxonomic groups preferring conditions associated with open canopies (e.g. hymenopterans and hoverflies), whereas ground-dwelling groups and/or groups typically associated with shady conditions (e.g. epigeic lichens and mycorrhizal fungi) were more likely to be negatively impacted by disturbance. Across all taxonomic groups, the highest α-diversity in disturbed forest patches occurred under moderate disturbance severity, i.e. with approximately 55% of trees killed by disturbance. We further extended our meta-analysis by applying a unified diversity concept based on Hill numbers to estimate α-diversity changes in different taxonomic groups across a gradient of disturbance severity measured at the stand scale and incorporating other disturbance features. We found that disturbance severity negatively affected diversity for Hill number q = 0 but not for q = 1 and q = 2, indicating that diversity–disturbance relationships are shaped by species relative abundances. Our synthesis of α-diversity was extended by a synthesis of disturbance-induced change in species assemblages, and revealed that disturbance changes the β-diversity of multiple taxonomic groups, including some groups that were not affected at the α-diversity level (birds and woody plants). Finally, we used mixed rarefaction/extrapolation to estimate biodiversity change as a function of the proportion of forests that were disturbed, i.e. the disturbance extent measured at the landscape scale. The comparison of intact and naturally disturbed forests revealed that both types of forests provide habitat for unique species assemblages, whereas species diversity in the mixture of disturbed and undisturbed forests peaked at intermediate values of disturbance extent in the simulated landscape. Hence, the relationship between α-diversity and disturbance severity in disturbed forest stands was strikingly similar to the relationship between species richness and disturbance extent in a landscape consisting of both disturbed and undisturbed forest habitats. This result suggests that both moderate disturbance severity and moderate disturbance extent support the highest levels of biodiversity in contemporary forest landscapes., British Ecological Society LRB20/1002, Junta de Andalucia, European Commission B-FQM-366-UGR20, Centro ANID Basal FB210015, Direccion de Investigacion Universidad de La Frontera DIUFRO DI20-0066, Federal Ministry of Education & Research (BMBF), Max Planck Society, INCT Madeiras da Amazonia, Federal Ministry of Education & Research (BMBF) 01LB1001A 01LK1602A, Brazilian Ministry of Science, Technology and Innovation (MCTI/FINEP) 01.11.01248.00, Russian Science Foundation (RSF) 21-14-00227, Ministry of Education, Youth & Sports - Czech Republic Czech Republic Government LTC 20058, Czech Academy of Sciences RVO67985939, UK Research & Innovation (UKRI), Natural Environment Research Council (NERC) GR3/11743, Greek project POL-AEGIS, Program THALES MIS 376737, Projekt DEAL TH 2218/5-1

Marine lakes represent a unique and globally rare aquatic environment characterised by lower salinities and pH and higher temperatures than the surrounding open water environment. Here we provide baseline data on planktonic communities of Archaea, Bacteria and microeukaryotes inside and outside (open water habitat) of three marine lakes (Kakaban, Haji Buang and Tanah Bamban) in the Berau region of Indonesia. Compositional variation was highly congruent with the major axis of variation separating open water from marine lake samples for all three domains. Planktonic Archaea mainly consisted of OTUs assigned to Euryarchaeota that were closely related to organisms in Genbank previously obtained from seawater samples. The majority of archaeal OTUs were most abundant in open water habitat with a few OTUs abundant in all habitats. Most bacterial sequences were assigned to Proteobacteria, Cyanobacteria and Bacteroidetes with the percentage of Cyanobacteria highest in two of the marine lakes and lowest in the remaining lake (Tanah Bamban). In contrast to Archaea, there were a number of bacterial OTUs that were markedly more abundant in marine lake habitat. Most microeukaryote sequences were assigned to the Alveolata, Stramenopiles, Opisthokonta, Archaeplastida and Hacrobia. As was the case with Bacteria, a number of abundant microeukaryote OTUs were more abundant in marine lake habitat. Our results thus indicate similar compositional responses to the environmental conditions in marine lake habitat across the major domains of life and point to marine lakes harbouring distinct microbial communities.

Aim To evaluate the interactive effects of oil contamination and chemical dispersant application on bacterial composition and sediment remediation of an estuarine port environment. Methods and results A multifactorial controlled microcosm experiment was set up using sediment cores retrieved from an estuarine port area located at Ria de Aveiro lagoon (Aveiro, Portugal). An oil spill with and without chemical dispersant addition was simulated. Sediment oil hydrocarbon concentrations and benthic bacterial community structure were evaluated by GC-MS and 16S rRNA high-throughput sequencing respectively. Although initially (first 10 days) chemical dispersion of oil enhanced the concentrations of the heavier polycyclic aromatic hydrocarbons and of the C22 -C30 alkane group, with time (21 days), no significant differences in hydrocarbon concentrations were detected among treatments. Moreover, no significant changes were detected in the structure of sediment bacterial communities, which mainly consisted of operational taxonomic units related to hydrocarbon-contaminated marine environments. We hypothesize that the environmental background of the sampling site preconditioned the communities' response to additional contamination. Conclusion This experimental microcosm study showed that the chemical dispersion of oil did not influence sediment remediation or bacterial community composition. Significance and impact of the study Our study showed that chemical dispersion of oil may not improve the remediation of port sediments. Further studies are needed to investigate the impact of chemical dispersants in combination with bioremediation strategies on the process of sediment remediation in port areas.

Assess microeukaryote community composition in seawater and sponge samples from Taiwanese coral reefs. In the present study, we used Illumina sequencing to explore the microeukaryote communities of seven biotopes (six sponge species and seawater) sampled in the Penghu archipelago of Taiwan. Microeukaryote communities were dominated by Dinoflagellates with Dinophyceae and Syndiniales well represented in all biotopes. Other abundant taxa included metazoa, red and green algae and Radiolaria. The only significant differences were a significantly higher relative abundance of Picobiliphyta and Stramenopiles_X in seawater and Metamonada in the sponge Acanthostylotella cornuta. There was also a significant difference in composition among biotopes with samples from sponges and seawater forming distinct clusters. There was, however, no congruence between prokaryote and microeukaryote community composition. After removing all OTUs 99.5% of sequences were shared between sponge and seawater samples. This data in the present study would appear to suggest that marine microeukaryote communities in sponges are largely derived from the surrounding seawater. Abundant OTUs were also related to organisms previously retrieved from seawater. A number of these OTUs though had relatively low sequence similarity to organisms in GenBank suggesting that more research of the microeukaryote communities in the Penghu archipelago may yield novel organisms in this relatively unexplored area.

Marine lakes are characterized by higher temperatures and lower pH and salinity values compared to open-water environments. Microbial communities in these habitats are, thus, subjected to d...

In the present study, prokaryotic communities from nine sponge species, two octocoral species, sediment and seawater were assessed from Maldivian coral reefs. All host species contained prokaryotic communities, which were distinct from those found in sediment and seawater. Certain host species, however, contained relatively high abundances of environmental OTUs, that is, OTUs recorded in sediment and/or seawater. This was particularly the case for the sponge species Svenzea novo sp. and Stylissa carteri with respect to seawater and Liosina paradoxa with respect to sediment. The sponge species Svenzea novo sp., S. carteri, L. paradoxa, Jaspis splendens and Ptilocaulis cf. spiculifer all had relatively high abundances of Proteobacteria, Cyanobacteria and Planctomycetes and relatively low evenness compared to the remaining sponge species. They also housed distinct subsets of highly abundant OTUs, which were rare or absent in other hosts, a trait they shared with the octocoral species. The aforementioned compositional traits suggest LMA status for these sponge species. The remaining species (Hyrtios erectus, Luffariella variabilis, Neopetrosia chaliniformis and Plakortis cf. kenyensis) had high relative abundances of Chloroflexi, Actinobacteria, Acidobacteria, Gemmatimonadetes, PAUC34f (or SAUL; sponge‐associated unclassified lineage) and Poribacteria, high evenness and limited compositional variation among samples, traits associated with HMA status. Our results, furthermore, confirmed the previously established classification of H. erectus as an HMA and S. carteri as a LMA species. Both octocoral species (Melithaea maldivensis and Paraminabea sp.) housed prokaryotic communities, which were compositionally distinct from sponge species and included significantly discriminating OTUs assigned to the Tenericutes, Spirochaetae and Proteobacteria phyla and the genera Mycoplasma (Tenericutes), Spirochaeta 2 (Spirochaetae) and Endozoicomonas (Proteobacteria).

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear how generalizable these relationships are across ecosystems, taxa and spatial scales. To address this gap, we collated 80 datasets from trait-based studies into a global database for metaCommunity Ecology: Species, Traits, Environment and Space; “CESTES”. Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available. By its harmonized structure, and the diversity of ecosystem types, taxonomic groups, and spatial scales it covers, the CESTES database provides an important opportunity for synthetic trait-based research in community ecology., Measurement(s)species abundance • species trait • environmental feature • latitude • longitudeTechnology Type(s)digital curationFactor Type(s)year of data collection • type of ecosystem • level of human disturbanceSample Characteristic - Environmentterrestrial natural environment • fresh water • marine biome • anthropogenic terrestrial biome • natural environment • area of mixed forest • cultivated environmentSample Characteristic - LocationEarth (planet) Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.11317790

The use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear how generalizable these relationships are across ecosystems, taxa and spatial scales. To address this gap, we collated 80 datasets from trait-based studies into a global database for metaCommunity Ecology: Species, Traits, Environment and Space; “CESTES”. Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available. By its harmonized structure, and the diversity of ecosystem types, taxonomic groups, and spatial scales it covers, the CESTES database provides an important opportunity for synthetic trait-based research in community ecology., This work was funded by the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig (funded by the German Research Foundation; DFG FZT 118). We thank Jitendra Gaikwad for his precious help with the technical aspects of the database storage and management through the iDiv Biodiversity Portal (https://idata.idiv.de/, https://doi.org/10.25829/idiv.286-21-2695) and the iDiv IT Support for their help in the CESTES website development (https://icestes.github.io/). The datasets provided by A. Jeliazkov were collected with financial support from the Fédération d’Ile-de-France pour la Recherche en Environnement (FIRE FR-3020). The dataset provided by R. Carvalho and F.L. Tejerina-Garro had financial support from the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq No. 471283/2006-1) granted to FLTG. The datasets provided by R. van Klink, J.-Y. Humbert, R. Arlettaz and M.H.M. Menz were collected with financial support from the Swiss National Science Foundation (grants 31003A_125398/2 and 31003A_149656) awarded to RA.

Purpose Marine lakes are unique habitats that house diverse assemblages of benthic and planktonic organisms including endemic species. In this study, we aimed to assess to what extent geographical location (Berau versus Papua) and the degree of marine lake connectivity (relatively open versus closed) to the surrounding marine environment structures the prokaryotic community composition of the sponge species Suberites diversicolor. Methods Sponge specimens were sampled in five marine lakes in Borneo and Papua and one open sea habitat in Taiwan. Result Prokaryotic communities of S. diversicolor were dominated by members assigned to the Proteobacteria (particularly Alphaproteobacteria and Gammaproteobacteria) and Cyanobacteria, which together made up from 78 to 87% of sequences in all samples. The dominant operational taxonomic units (OTUs) in most samples, OTUs 1 and 3, were both assigned to the alphaproteobacterial order Rhodospirillales with OTU-1 dominant in the marine lakes of Berau and Papua and OTU-3 in Taiwan. OTU-3 was also largely absent from Papuan samples but present in all Berau samples. Compositionally, S. diversicolor samples clustered according to geographical location with the main axis of variation separating marine lake samples collected in Berau from those collected in Papua and the second axis of variation separating open sea samples collected in Taiwan from all marine lake samples. In addition, our results suggest that the degree of lake connectivity to the open sea also influences prokaryotic composition. Conclusion Although previous studies have shown that sponge-associated microbial communities tend to be stable across different geographical and environmental gradients, in the present study, both geography and local environmental conditions were significant predictors of variation in prokaryotic community composition of S. diversicolor.

Marine lakes are landlocked bodies of seawater, isolated to varying degrees from the surrounding marine habitat. Isolated lakes generally have lower pH values, salinities and higher temperatures than more open lakes. We used a 16S rRNA gene barcoded pyrosequencing approach to study the bacterial communities of two sponge species, sediment and seawater in one enclosed and two open marine lakes. Bacterial communities of the sponge Spheciospongia solida mainly consisted of Proteobacteria, Cyanobacteria and Bacteroidetes. In contrast, Proteobacteria, Chloroflexi and Acidobacteria dominated the bacterial communities of the sponge Spongia ceylonensis. Although only a limited amount of samples were collected, both water and S. ceylonensis sponge had higher relative abundances of Cyanobacteria in the enclosed lake, which mainly consisted of OTUs assigned to the genus Synechococcus. This is in line with a number of previous studies, which have shown that environmental conditions found within low pH environments such as marine lakes benefit the growth of Synechococcus spp. Future studies should address the mechanism by which Synechococcus spp. may help host sponges and their bacterial communities adapt to low pH conditions in isolated marine lakes and other low-pH environments. published

Ocean acidification may exacerbate the environmental impact of oil hydrocarbon pollution by disrupting the core composition of the superficial (0-1 cm) benthic bacterial communities. However, at the subsurface sediments (approximately 5 cm below sea floor), the local biochemical characteristics and the superjacent sediment barrier may buffer these environmental changes. In this study, we used a microcosm experimental approach to access the independent and interactive effects of reduced seawater pH and oil contamination on the composition of subsurface benthic bacterial communities, at two time points, by 16S rRNA gene-based high-throughput sequencing. An in-depth taxa-specific variance analysis revealed that the independent effects of reduced seawater pH and oil contamination were significant predictors of changes in the relative abundance of some specific bacterial groups (e.g., Firmicutes, Rhizobiales, and Desulfobulbaceae). However, our results indicated that the overall microbial community structure was not affected by independent and interactive effects of reduced pH and oil contamination. This study provides evidence that bacterial communities inhabiting subsurface sediment may be less susceptible to the effects of oil contamination in a scenario of reduced seawater pH.

In the present study, we used Illumina sequencing to explore the prokaryote communities of 17 demosponge species and how they compare with bacterial mat, sediment and seawater samples (all sampled from coral reef habitat in Taiwan and Thailand). The studied sponge species formed three clusters. OTU richness and evenness were by far highest in the sediment and bacterial mat biotopes. There were pronounced differences in OTU richness and evenness among clusters and also considerable variation among certain host species within clusters. Additionally, the relative abundance of some prokaryotic taxa also differed among clusters with Poribacteria, for example, being recorded in all sponge species, but with very low relative abundances in species of two of the three clusters. This sponge-associated phylum was, however, recorded at relatively high mean abundance in bacterial mat samples, which also housed relatively high abundances of actinobacterial and Chloroflexi members. Our results support the HMA status of the species Aaptos lobata, Hyrtios erectus, Pseudoceratina purpurea and Xestospongia testudinaria, which clustered together and LMA status of the species Acanthella cavernosa, Echinodictyum asperum, Jaspis splendens, Ptilocaulis spiculifer, Stylissa carteri and Suberites diversicolor, which also clustered together. Other species (Agelas cavernosa, Agelas nemoechinata, Acanthostylotella cornuta, Paratetilla sp., Hymeniacidon sp. and Haliclona cymaeformis) deviated somewhat from the typical HMA/LMA dichotomy and formed a strongly supported cluster.

Forest fires pose an important threat to tropical rain-forest biodiversity. In the present study, we assessed ground layer (herb and shrub) communities in six differentially disturbed landscape plots in East Kalimantan, Indonesia, including primary and logged forest and once-, twice- and frequently-burnt forest. Overall, we recorded 175 species of herbs and shrubs; richness was highest in twice-burnt forest and lowest in logged forest. Vegetation and topographical variables including the percentage of the plot burnt and tree abundance were significant predictors of variation in composition. The main compositional gradient showed a clear distinction between subplots in unburnt versus burnt forest. A subset of subplots in burnt forest, however, clustered together with subplots from unburnt forest. These plots were located in a network of relatively unscathed forest along floodplains that persisted in the burnt-forest matrix. Small plant species associated with unburnt forest included several species of Dryopteridaceae, Marantaceae and Rubiaceae. Species associated with once- and twice-burnt forest included Mikania scandens (Compositae), Microlepia speluncae (Dennstaedtiaceae), Nephrolepis cf. biserrata (Nephrolepidaceae), Lygodium microphyllum (Schizaeaceae) and Hornstedtia cf. reticulata (Zingiberaceae). The frequently-burnt landscape plot was characterized by a high cover of the grass species Imperata cylindrica and the invasive exotic shrub Chromolaena odorata. Importantly, these species and other exotics had also invaded the once- and twice-burnt forest and represent a potential threat to forest recovery.

The stressful conditions of intensive aquaculture systems, combined with excessive antibiotic use, may have dysbiotic effects on aquaculture microbiomes and promote the spread of opportunistic pathogens. Here, we hypothesized that humic substances (HS), when added to the rearing water of a marine recirculating aquaculture system (RAS), will act as a chemical modulator of fish-associated bacterial communities and suppress potential pathogens. To test this, a 28-day RAS trial for juvenile European sea bass (Dicentrarchus labrax) was conducted with and without HS modulation. High-throughput sequencing of the 16S rRNA gene was used to evaluate role of HS in modulating fish bacterial assemblages (gut and skin mucus). In addition to this, biometric, digestive and oxidative stress parameters were measured to assess the impact of HS on fish performance. HS modulation was associated with an increased bacterial diversity and a distinct bacterial community composition in the fish skin mucus. HS modulation significantly increased the relative abundance of amplicon sequence variants (ASVs) related to the potentially beneficial Roseobacter clade and lowered the abundances of ASVs related to potential fish pathogens (e.g., Acinetobacter jonhsonii and Vibrio harveyi). In line with compositional differences, there was an enrichment of predictive KEGG categories related to antagonism and significantly lower abundances of KEGG categories related to pathogenesis and invasibility. In the fish gut, HS modulation was associated with a lower abundance of the orders Enterobacteriales and Bacillales. HS modulation also was associated with significant reductions in fish oxidative stress parameters and a significant increase in the activity of the digestive enzyme chymotrypsin. For the first time, our results demonstrate the potential of dissolved HS as a modulator of fish microbial communities.

In the present study, the impact of logging was assessed on the forest structure, richness, and composition of trees, lianas, and ground herbs in Indonesian Borneo. There were no significant differ...

Three species of giant barrel sponge are currently recognized in two distinct geographic regions, the tropical Atlantic and the Indo-Pacific. In this study, we used molecular techniques to study populations of giant barrel sponges across the globe and assessed whether the genetic structure of these populations agreed with current taxonomic consensus or, in contrast, whether there was evidence of cryptic species. Using molecular data, we assessed whether giant barrel sponges in each oceanic realm represented separate monophyletic lineages. Giant barrel sponges from 17 coral reef systems across the globe were sequenced for mitochondrial (partial CO1 and ATP6 genes) and nuclear (ATPsβ intron) DNA markers. In total, we obtained 395 combined sequences of the mitochondrial CO1 and ATP6 markers, which resulted in 17 different haplotypes. We compared a phylogenetic tree constructed from 285 alleles of the nuclear intron ATPsβ to the 17 mitochondrial haplotypes. Congruent patterns between mitochondrial and nuclear gene trees of giant barrel sponges provided evidence for the existence of multiple reproductively isolated species, particularly where they occurred in sympatry. The species complexes in the tropical Atlantic and the Indo-Pacific, however, do not form separate monophyletic lineages. This rules out the scenario that one species of giant barrel sponge developed into separate species complexes following geographic separation and instead suggests that multiple species of giant barrel sponges already existed prior to the physical separation of the Indo-Pacific and tropical Atlantic.

Previously, it was believed that the prokaryote communities of typical ‘low-microbial abundance’ (LMA) or ‘non-symbiont harboring’ sponges were merely subsets of the prokaryote plankton community. Recent research has, however, shown that these sponges are dominated by particular clades of Proteobacteria or Cyanobacteria. Here, we expand on this research and assess the composition and putative functional profiles of prokaryotic communities from LMA sponges collected in two ecosystems (coral reef and hydrothermal vent) from vicinal islands of Taiwan with distinct physicochemical conditions. Six sponge species identified as Acanthella cavernosa (Bubarida), Echinodictyum asperum, Ptilocaulis spiculifer (Axinellida), Jaspis splendens (Tetractinellida), Stylissa carteri (Scopalinida) and Suberites sp. (Suberitida) were sampled in coral reefs in the Penghu archipelago. One sponge species provisionally identified as Hymeniacidon novo spec. (Suberitida) was sampled in hydrothermal vent habitat. Each sponge was dominated by a limited set of operational taxonomic units which were similar to sequences from organisms previously obtained from other LMA sponges. There was a distinct bacterial community between sponges collected in coral reef and in hydrothermal vents. The putative functional profile revealed that the prokaryote community from sponges collected in hydrothermal vents was significantly enriched for pathways related to DNA replication and repair. published

The present study aims to assess the plastic response of Zostera noltei meadows traits under spatio-temporal shifts in salinity combined with sediment environmental variables (temperature; pH; loss-on-ignition (LOI); carbon (C) and nitrogen (N) pools (top 5 cm)). Z. noltei biomass, C and N pools, leaf photosynthetic performance and esterified fatty acid (FA) profile were assessed within a temperate coastal lagoon during winter and late spring, along sites spatially distributed. None of the surveyed traits for Z. noltei displayed a clear spatial trend. Z. noltei proved to be euryhaline, whose biology was only slightly affected within this salinity range, in each season (14–39 in winter; 33–41 in late spring). Seasonal differences in salinity and environmental parameters explain the differences recorded in Z. noltei traits (aboveground biomass, N and C pools; photosynthetic performance). Spatio-temporal salinity shifts did not significantly affect the pool of FA present in Z. noltei. Overall, within the salinity range surveyed, the ecological processes studied and regulating Z. noltei meadows do not appear to be at risk. This work reinforces the plasticity of Z. noltei to salinity shifts within the studied range, with this finding being particularly relevant in the context of extreme weather events (e.g., winter freshwater floods, summer droughts).

Little is known about the microbial diversity, composition and predicted functional similarities and dissimilarities between prokaryotic kingdoms and among coral reef biotopes located in close spatial proximity to one other. In this study, we compared communities of Archaea and Bacteria in two distinct biotopes, namely, the sponge Xestospongia testudinaria and sediment of the Berau reef system, Indonesia. Using a 16S rRNA gene barcoded pyrosequencing approach and a recently developed predictive metagenomic approach (PICRUSt), we tested to what extent sediment and X . testudinaria host compositionally and functionally distinct communities of Archaea and Bacteria. Although Crenarchaeota (Archaea) and Proteobacteria (Bacteria) were the dominant phyla in the microbial communities of both sediment and sponge, there were significant differences in composition between them. Biotope proved to be the main identifiable factor affecting composition. In line with the compositional differences between sediment and sponge prokaryote communities, there were also differences in predicted functions. The archaeal and bacterial communities of sediment were enriched for functions associated with the Metabolism and Environmental Information Processing categories; those of X . testudinaria were enriched for functions associated with the Genetic Information Processing category. The significant levels of concordance between archaeal and bacterial communities and the similar enrichment of these communities in the same functional categories suggests a certain degree of functional redundancy between Archaea and Bacteria in the studied biotopes, which for the sponge may result in an increased resilience to environmental perturbations.

In a previous study, we identified host species that housed high and low diversity prokaryotic communities. In the present study, we expand on this and assessed the prokaryotic communities associated with seawater, sediment and 11 host species from 7 different phyla in a Taiwanese coral reef setting. The host taxa sampled included hard, octo- and black corals, molluscs, bryozoans, flatworms, fish and sea urchins. There were highly significant differences in composition among host species and all host species housed distinct communities from those found in seawater and sediment. In a hierarchical clustering analysis, samples from all host species, with the exception of the coral Galaxea astreata, formed significantly supported clusters. In addition to this, the coral G. astreata and the bryozoan Triphyllozoon inornatum on the one hand and the coral Tubastraea coccinea, the hermit crab Calcinus laevimanus and the flatworm Thysanozoon nigropapillosum on the other formed significantly supported clusters. In addition to composition, there were highly pronounced differences in richness and evenness among host species from the most diverse species, the bryozoan T. inornatum at 2518 ± 240 OTUs per 10,000 sequences to the least diverse species, the octocoral Cladiella sp. at 142 ± 14 OTUs per 10,000 sequences. In line with the differences in composition, there were significant differences in predicted metagenomic gene counts among host species. Furthermore, there were pronounced compositional and predicted functional differences between high diversity hosts (Liolophura japonica, G. astreata, T. coccinea, C. laevimanus, T. inornatum) and low diversity hosts (Antipathes sp., Pomacentrus coelestis, Modiolus auriculatus, T. nigropapillosum, Cladiella sp. and Diadema savigny). In particular, we found that all tested low diversity hosts were predicted to be enriched for the phosphotransferase system compared to high diversity hosts.

Much recent marine microbial research has focused on sponges, but very little is known about how the sponge microbiome fits in the greater coral reef microbial metacommunity. Here, we present an extensive survey of the prokaryote communities of a wide range of biotopes from Indo-Pacific coral reef environments. We find a large variation in operational taxonomic unit (OTU) richness, with algae, chitons, stony corals and sea cucumbers housing the most diverse prokaryote communities. These biotopes share a higher percentage and number of OTUs with sediment and are particularly enriched in members of the phylum Planctomycetes. Despite having lower OTU richness, sponges share the greatest percentage (>90%) of OTUs with >100 sequences with the environment (sediment and/or seawater) although there is considerable variation among sponge species. Our results, furthermore, highlight that prokaryote microorganisms are shared among multiple coral reef biotopes, and that, although compositionally distinct, the sponge prokaryote community does not appear to be as sponge-specific as previously thought., Here the authors holistically examine prokaryote communities associated with diverse coral reef hosts, including sponges, nudibranchs, sea cucumbers, and corals. The results show that sponges have a relatively low diversity of prokaryotes, most of which are shared across a wide range of host taxa rather than being sponge-specific.

In the present study, we assessed prokaryotic communities of demosponges, a calcareous sponge, octocorals, sediment and seawater in coral reef habitat of the central Red Sea, including endemic species and species new to science. Goals of the study were to compare the prokaryotic communities of demosponges with the calcareous sponge and octocorals and to assign preliminary high microbial abundance (HMA) or low microbial abundance (LMA) status to the sponge species based on compositional trait data. Based on the compositional data, we were able to assign preliminary LMA or HMA status to all sponge species. Certain species, however, had traits of both LMA and HMA species. For example, the sponge Ectyoplasia coccinea, which appeared to be a LMA species, had traits, including a relatively high abundance of Chloroflexi members, that were more typical of HMA species. This included dominant OTUs assigned to two different classes within the Chloroflexi. The calcareous sponge clustered together with seawater, the known LMA sponge Stylissa carteri and other presumable LMA species. The two dominant OTUs of this species were assigned to the Deltaproteobacteria and had no close relatives in the GenBank database. The octocoral species in the present study had prokaryotic communities that were distinct from sediment, seawater and all sponge species. These were characterised by OTUs assigned to the orders Rhodospirillales, Cellvibrionales, Spirochaetales and the genus Endozoicomonas, which were rare or absent in samples from other biotopes.

The importance of microbial diversity and their role in the maintenance of fish health in aquaculture systems has been increasingly recognized in recent years. However, there is still a major knowledge gap regarding the ecology, composition and dynamics of microbial plankton assemblages during fish production. In this study, we aimed to investigate the seasonal dynamics and potential interactions of bacterial and microeukaryotic plankton communities in a semi-intensive aquaculture for European sea bass (Dicentrarchus labrax) cultured together with low density of gilthead sea bream (Sparus aurata) over a one-year period (January/2014 – November/2014). While the most abundant bacterial classes were Gammaproteobacteria, Flavobacteriia and Alphaproteobacteria; microeukaryotic communities were dominated by Ochrophyta, Chlorophyta and Ciliophora groups. Temperature and salinity were identified as significant drivers of the overall microbial community composition, which varied congruently along the seasons. However, while the dominant (more abundant) groups of bacteria occurred in the warmest months, the dominant groups of microeukaryotes occurred in the coldest months. There was also an inverse relationship between abundances of grazers and bacterial operational taxonomic units (OTUs). Overall, besides the potential effects of the abiotic parameters on the microbial plankton communities, the correlation between bacteria and microeukaryotic populations observed here may be an indication of trophic and/or metabolic interdependence between these two domains. Future studies should focus on the underlying mechanisms of this interdependence for a better understand of the impact of microeukaryotic communities on aquaculture bacterioplankton structure and function. In addition, this knowledge could be of interest in the development of microbial management strategies for aquaculture systems.

There is a growing consensus that future technological developments of aquaculture systems should account for the structure and function of microbial communities in the whole system and not only in fish guts. In this study, we aimed to investigate the composition of bacterioplankton communities of a hatchery recirculating aquaculture system (RAS) used for the production of Senegalese sole (Solea senegalensis) juveniles. To this end, we used a 16S rRNA gene based denaturing gradient gel electrophoresis (DGGE) and pyrosequencing analyses to characterize the bacterioplankton communities of the RAS and its water supply. Overall, the most abundant orders were Alteromonadales, Rhodobacterales, Oceanospirillales, Vibrionales, Flavobacteriales, Lactobacillales, Thiotrichales, Burkholderiales and Bdellovibrionales. Although we found a clear distinction between the RAS and the water supply bacterioplankton communities, most of the abundant OTUs (≥50 sequences) in the hatchery RAS were also present in the water supply. These included OTUs related to Pseudoalteromonas genus and the Roseobacter clade, which are known to comprise bacterial members with activity against Vibrio fish pathogens. Overall, in contrast to previous findings for sole grow-out RAS, our results suggest that the water supply may influence the bacterioplankton community structure of sole hatchery RAS. Further studies are needed to investigate the effect of aquaculture practices on RAS bacterioplankton communities and identification of the key drivers of their structure and diversity.

In Indonesia and elsewhere, Imperata cylindrica grassland now covers millions of hectares of land previously covered by rain forest. In the present study, shrubs, trees and climbers were recorded in sixteen 10 × 20-m plots and herb cover (ferns, grasses and herbaceous dicots) estimated in nested 2 × 2-m subplots. Butterflies and odonates were netted along 300-m transects. All plots and transects were randomly allocated to a 450 ha, I. cylindrica-dominated landscape. A total of 43 shrub, tree and climber, 16 herb, 67 butterfly and 30 odonate species were recorded. Shrubs, trees and climbers were present throughout the study area, but basal area was very low and mainly consisted of invasive species. Imperata cylindrica covered an estimated 65% of the area with other plant species or bare soil covering the remainder. Butterfly and odonate communities mainly consisted of species with large geographic distributions, but some recorded species had more limited distributions. The latter were, however, species known to associate with perturbed forest environments. Variation in the composition of butterflies and odonates was also related to variation in habitat structure (e.g. altitude and slope) and plant composition. Plant composition in particular appeared to structure both butterfly and odonate communities.

Most existing coral reef studies have focused on a single biotope and a single domain (Archaea or Bacteria). Few coral reef studies have explored the archaeal and bacterial community simultaneously. In this study, we compare the diversity and composition of archaeal and bacterial communities in seawater and two closely related sponge species (Stylissa carteri and Stylissa massa) in the Berau reef system, Indonesia. A 16S rRNA gene barcoded pyrosequencing approach was used to test to what extent seawater, S. carteri and S. massa host compositionally distinct communities of Archaea and Bacteria. Proteobacteria dominated the bacterial communities of all three studied biotopes whereas Euryarchaeota was the most abundant archaeal phylum in seawater and Crenarchaeota the most abundant archaeal phylum in both Stylissa species. Biotopes explained 56% and 53% of the variation in archaeal and bacterial composition respectively and there was significant congruence between the composition of archaeal and bacterial communities. These results suggest that the processes that drive bacterial composition within the studied biotopes may be fundamentally similar to those that drive archaeal composition.

Substrate cover, water quality parameters and assemblages of corals, fishes, sponges, echinoderms, ascidians, molluscs, benthic foraminifera and macroalgae were sampled across a pronounced environmental gradient in the Jakarta Bay–Thousand Islands reef complex. Inshore sites mainly consisted of sand, rubble and turf algae with elevated temperature, dissolved oxygen, pH and chlorophyll concentrations and depauperate assemblages of all taxa. Live coral cover was very low inshore and mainly consisted of sparse massive coral heads and a few encrusting species. Faunal assemblages were more speciose and compositionally distinct mid- and offshore compared to inshore. There were, however, small-scale differences among taxa. Certain midshore sites, for example, housed assemblages resembling those typical of the inshore environment but this differed depending on the taxon. Substrate, water quality and spatial variables together explained from 31% (molluscs) to 72% (foraminifera) of the variation in composition. In general, satellite-derived parameters outperformed locally measured parameters.

Assemblages of corals, sponges, foraminifera, sediment bacteria and sediment archaea were assessed at two depths in the Spermonde Archipelago. Our goal was to assess to what extent variation in composition could be explained by habitat and water quality variables. The habitat variables consisted of depth, substrate type and scleractinian coral cover while water quality variables were derived from ocean color satellite imagery, including the colored dissolved organic matter index (CDOM), chlorophyll-a (Chlor-a) and remote sensing reflectance at 645n m (Rrs_645). Together, habitat and water quality variables explained from 31% (sediment bacteria) to 80% (forams) of the variation in composition. The variation in composition of corals, sponges, forams and sediment archaea was primarily related to habitat variables, while the variation in composition of sediment bacteria was primarily related to water quality variables. Habitat and water quality variables explained similar amounts of variation in the composition of corals and sediment bacteria. CDOM (sponges, sediment bacteria and sediment archaea), Chlor-a (corals and forams) and Rrs_645 (sponges and forams) proved significant predictors of variation in composition for the studied taxa. In addition to water quality variables, all taxa responded to a range of habitat variables including depth and the percentage cover of various benthic life forms including coral cover variables, rubble and sand. Sand cover was the most important habitat variable for corals, sponges, sediment bacteria and sediment archaea. Coral life forms including the cover of branching and tabular corals were important habitat variables for sponges and forams. These results show marked differences in how various taxa respond to variation in habitat and water quality in the Spermonde Archipelago. Moreover, our results indicate that variables estimated from ocean color satellite imagery proved to be better predictors of variation in marine community composition than commonly-used proxies such as the distance offshore or distance to the nearest river.

Sponges harbor complex communities of microorganisms that carry out essential roles for the functioning and survival of their hosts. In some cases, genetically related sponges from different geographic regions share microbes, while in other cases microbial communities are more similar in unrelated sponges collected from the same location. To better understand how geography and host phylogeny cause variation in the prokaryotic community of sponges, we compared the prokaryotic community of 44 giant barrel sponges (Xestospongia spp.). These sponges belonged to six reproductively isolated genetic groups from eight areas throughout the Indo-Pacific region. Using Illumina sequencing, we obtained 440 000 sequences of the 16S rRNA gene V3V4 variable region that were assigned to 3795 operational taxonomic units (OTUs). The prokaryotic community of giant barrel sponges was characterized by 71 core OTUs (i.e. OTUs present in each specimen) that represented 57.5% of the total number of sequences. The relative abundance of these core OTUs varied significantly among samples, and this variation was predominantly related to the geographic origin of the sample. These results show that in giant barrel sponges, the variation in the prokaryotic community is primarily associated with geography as opposed to phylogenetic relatedness., The prokaryotic communities of multiple giant barrel sponge species in the Indo-Pacific are more strongly influenced by geography than host phylogeny.

The intensification of marine aquaculture raises multiple sustainability issues, namely the handling of nutrient-rich effluents that can adversely impact ecosystems. As integrated multi-trophic aquaculture (IMTA) gains momentum, the use of halophyte plants to phytoremediate aquaculture effluents has received growing attention, particularly in aquaponics. It is, therefore, important to obtain a more in-depth knowledge of the microbial communities present in the root systems of these plants, both in their natural environment (sediment) and in aquaponics, in order to understand their nutrient removal potential. The present study used denaturing gradient gel electrophoresis (DGGE) and barcoded pyrosequencing to assess the bacterial community present in the endosphere and rhizosphere of three halophyte plants: Halimione portulacoides, Salicornia ramosissima and Sarcocornia perennis. Species-specific effects were recorded in the profile and diversity of the bacterial communities present in halophyte roots, with significant differences also recorded for the same halophyte species grown in contrasting environments (sediment vs. aquaponics). In aquaponics the most abundant groups belonged to the orders Rhodocyclales, Campylobacterales, Rhodobacterales and Desulfobacterales, while in the natural environment (sediment) the most abundant groups belonged to the orders Rhizobiales, Sphingomonadales and Alteromonadales. An overall enrichment in bacterial taxa involved in nutrient cycling was recorded in the roots of halophytes grown in aquaponics (such as Denitromonas, Mesorhizobium, Colwellia, Dokdonella and Arcobacter), thereby highlighting their potential to reduce the nutrient loads from aquaculture effluents.

Despite alterations caused by anthropogenic activities in Singaporean coral reefs, the sponge communities are quite diverse andXestospongia testudinariais one of the most common sponge species. In the present study, we used 16S rRNA gene barcoded pyrosequencing to characterize and compare bacterial communities from different biotopes (sponge, seawater and sediment) and to identify dominant bacterial symbionts ofX. testudinariain a Singaporean coral reef ecosystem. Our results showed that biotope appears to affect the richness, composition and abundance of bacterial communities. Proteobacteria was the most abundant phylum in sediment and seawater whilst Chloroflexi was more abundant inX. testudinaria.Members of the order Caldilineales (fermentation of organic substrates), Chromatiales (purple sulphur bacteria), Rhodospirillales (purple non-sulphur bacteria) and Syntrophobacterales (sulphate-reducing bacteria) were relatively more abundant inX. testudinariasamples.

Sponge species have been deemed high microbial abundance (HMA) or low microbial abundance (LMA) based on the composition and abundance of their microbial symbionts. In the present study, we evaluated the richness and composition of bacterial communities associated with one HMA sponge (Xestospongia testudinaria; Demospongiae: Haplosclerida: Petrosiidae), one LMA sponge (Stylissa carteri; Demospongiae: Scopalinida - Scopalinidae), and one sponge with a hitherto unknown microbial community (Aaptos suberitoides; Demospongiae: Suberitida: Suberitidae) inhabiting the Misool coral reef system in the West Papua province of Indonesia. The bacterial communities of these sponge species were also compared with seawater and sediment bacterial communities from the same coastal coral reef habitat. Using a 16S rRNA gene barcoded pyrosequencing approach, we showed that the most abundant phylum overall was Proteobacteria. The biotope (sponge species, sediment or seawater) explained almost 84% of the variation in bacterial composition with highly significant differences in composition among biotopes and a clear separation between bacterial communities from seawater and S. carteri; X. testudinaria and A. suberitoides and sediment. The Chloroflexi classes SAR202 and Anaerolineae were most abundant in A. suberitoides and X. testudinaria and both of these species shared several OTUs that were largely absent in the remaining biotopes. This suggests that A. suberitoides is a HMA sponge. Although similar, the bacterial communities of S. carteri and seawater were compositionally distinct. These results confirm compositional differences between sponge and non-sponge biotopes and between HMA and LMA sponges. published

The high/low microbial abundance (HMA/LMA) dichotomy in sponges has been the subject of several studies over recent years, but few studies have analysed this dichotomy in terms of the sponge archaeal community and function. Using a 16S rRNA gene barcoded pyrosequencing approach and predictive functional analysis (PICRUSt) we compared the archaeal composition, richness and predicted function of one HMA sponge (Xestospongia testudinaria), one LMA sponge (Stylissa carteri) and one sponge species of unknown microbial abundance (Aaptos lobata). Although most of the archaeal sequences were assigned to the Crenarchaeota phylum, S. carteri had the highest percentage of sequences assigned to the Euryarchaeota phylum. Variation among sponge species explained >85% of the variation in archaeal operational taxonomic unit (OTU) composition with each sponge species forming a distinct cluster. There were significant differences in predicted PICRUSt profiles among sponge species, suggesting that archaeal communities present in the studied sponge species may perform different functions. X. testudinaria and A. lobata were similar both in terms of OTU and KEGG orthologues composition, which may indicate that A. lobata is a HMA sponge. Additionally, some of the most enriched functions seem to be related to traits associated with high and low microbial abundance sponges. published