Search

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.

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...

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.

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.

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.

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...

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

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.

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.

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

In this study, we used a 16S rRNA gene barcoded pyrosequencing approach to sample bacterial communities from six biotopes, namely, seawater, sediment and four sponge species (Stylissa carteri, Stylissa massa, Xestospongia testudinaria and Hyrtios erectus) inhabiting coral reefs of the Spermonde Archipelago, South Sulawesi, Indonesia. Samples were collected along a pronounced onshore to offshore environmental gradient. Our goals were to (1) compare higher taxon abundance among biotopes, (2) test to what extent variation in bacterial composition can be explained by the biotope versus environment, (3) identify dominant (>300 sequences) bacterial operational taxonomic units (OTUs) and their closest known relatives and (4) assign putative functions to the sponge bacterial communities using a recently developed predictive metagenomic approach. We observed marked differences in bacterial composition and the relative abundance of the most abundant phyla, classes and orders among sponge species, seawater and sediment. Although all biotopes housed compositionally distinct bacterial communities, there were three prominent clusters. These included (1) both Stylissa species and seawater, (2) X. testudinaria and H. erectus and (3) sediment. Bacterial communities sampled from the same biotope, but different environments (based on proximity to the coast) were much more similar than bacterial communities from different biotopes in the same environment. The biotope thus appears to be a much more important structuring force than the surrounding environment. There were concomitant differences in the predicted counts of KEGG orthologs (KOs) suggesting that bacterial communities housed in different sponge species, sediment and seawater perform distinct functions. In particular, the bacterial communities of both Stylissa species were predicted to be enriched for KOs related to chemotaxis, nitrification and denitrification whereas bacterial communities in X. testudinaria and H. erectus were predicted to be enriched for KOs related to the toxin–antitoxin (TA) system, nutrient starvation and heavy metal export.

Sponge-related research in Taiwan has primarily focused on natural product exploration. This research has, however, been hampered by a lack of fundamental work on sponge taxonomy and ecology. In the present study, subtidal sponges were photo-recordedin situand collected by scuba diving at a depth range of 2–20 m from 2009 to 2012 in 16 different sites surrounding the Penghu Archipelago, Taiwan. Sponge samples were identified to the lowest taxonomic level based on skeletal morphology and spicules. A total of 53 species belonging to 24 families and 10 orders were identified in this study. The number of sponge species per site ranged from 0 to 24. The most widely distributed sponge species wasCallyspongia(Euplacella) cf.communis(Carter, 1881) followed byHaliclona(Gellius)cymaeformis(Esper, 1794), andAaptos suberitoides(Brøndsted, 1934). At one location, Chipeiyu, no sponges were observed. Non-metric multidimensional scaling (NMDS) ordination revealed relatively low similarity among most sampling sites. Large- and small-scale hydrological and habitat features are probably responsible for compositional variation of sponge assemblages among groups of sampling sites. Our richness analyses suggest that many more sponge species remain to be discovered in the Penghu Archipelago.

Anchialine lakes are a globally rare and unique ecosystem consisting of saline lakes surrounded by land and isolated from the surrounding marine environment. These lakes host a unique flora and fauna including numerous endemic species. Relatively few studies have, however, studied the prokaryote communities present in these lakes and compared them with the surrounding ‘open water’ marine environment. In the present study, we used a 16S rRNA gene barcoded pyrosequencing approach to examine prokaryote (Bacteria and Archaea) composition in three distinct biotopes (sediment, water and the mussel Brachidontes sp.) inhabiting four habitats, namely, three marine lakes and the surrounding marine environment of Berau, Indonesia. Biotope and habitat proved significant predictors of variation in bacterial and archaeal composition and higher taxon abundance. Most bacterial sequences belonged to OTUs assigned to the Proteobacteria. Compared to sediment and water, mussels had relatively high abundances of the classes Mollicutes and Epsilonproteobacteria. Most archaeal sequences, in turn, belonged to OTUs assigned to the Crenarchaeota with the relative abundance of crenarchaeotes highest in mussel samples. For both Bacteria and Archaea, the main variation in composition was between water samples on the one hand and sediment and mussel samples on the other. Sediment and mussels also shared much more OTUs than either shared with water. Abundant bacterial OTUs in mussels were related to organisms previously obtained from corals, oysters and the deepsea mussel Bathymodiolus manusensis. Abundant archaeal OTUs in mussels, in contrast, were closely related to organisms previously obtained from sediment.

Marine lakes are small bodies of landlocked seawater that are isolated from the open sea and have been shown to house numerous rare and unique taxa. The environmental conditions of the lakes are also characterised by lower pH and salinity and higher temperatures than generally found in the open sea. In the present study, we used a 16S rRNA gene barcoded pyrosequencing approach and a predictive metagenomic approach (PICRUSt) to examine bacterial composition and function in three distinct biotopes (sediment, water and the sponge species Biemna fortis) in three habitats (two marine lakes and the open sea) of the Berau reef system, Indonesia. Both biotope and habitat were significant predictors of higher taxon abundance and compositional variation. Most of the variation in operational taxonomic unit (OTU) composition was related to the biotope (42% for biotope alone versus 9% for habitat alone and 15% combined). Most OTUs were also restricted to a single biotope (1047 for B. fortis, 6120 for sediment and 471 for water). Only 98 OTUs were shared across all three biotopes. Bacterial communities from B. fortis, sediment and water samples were, however, also distinct in marine lake and open sea habitats. This was evident in the abundance of higher bacterial taxa. For example, the phylum Cyanobacteria was significantly more abundant in samples from marine lakes than from the open sea. This difference was most pronounced in the sponge B. fortis. In line with the compositional differences, there were pronounced differences in predicted relative gene count abundance among biotopes and habitats. Of particular interest was the predicted enrichment in B. fortis from the marine lakes for pathways including DNA replication and repair and the glutathione metabolism. This may facilitate adaptation of host and microbes to life in 'stressful' low pH, low salinity and/or high temperature environments such as those encountered in marine lakes.

Ria de Aveiro is a mesotidal coastal lagoon with one of the largest continuous salt marshes in Europe. The objective of this work was to assess C, N and P stocks of Spartina maritima (low marsh pioneer halophyte) and Juncus maritimus (representative of mid-high marsh halophytes) combined with the contribution of Halimione portulacoides, Sarcocornia perennis, and Bolbochenous maritimus to the lagoon ≈4400 ha marsh area. A multivariate analysis (PCO), taking into account environmental variables and the annual biomass and nutrient dynamics, showed that there are no clear seasonal or spatial differences within low or mid-high marshes, but clearly separates J. maritimus and S. maritima marshes. Calculations of C, N and P stocks in the biomass of the five most representative halophytes plus the respective rhizosediment (25 cm depth), and taking into account their relative coverage, represents 252053 Mg C, 38100 Mg N and 7563 Mg P. Over 90% of the stocks are found within mid-high marshes. This work shows the importance of this lagoon’s salt marshes on climate and nutrients regulation, and defines the current condition concerning the ‘blue carbon’ and nutrient stocks, as a basis for prospective future scenarios of salt marsh degradation or loss, namely under SLR context.

In this study, two molecular techniques [denaturing gradient gel electrophoresis (DGGE) and barcoded pyrosequencing] were used to evaluate the composition of bacterial communities in salt marsh microhabitats [bulk sediment and sediment surrounding the roots (rhizosphere) of Halimione portulacoides and Sarcocornia perennis ssp. perennis] that have been differentially affected by oil hydrocarbon (OH) pollution. Both DGGE and pyrosequencing revealed that bacterial composition is structured by microhabitat. Rhizosphere sediment from both plant species revealed enrichment of operational taxonomic units closely related to Acidimicrobiales, Myxococcales and Sphingomonadales. The in silico metagenome analyses suggest that homologous genes related to OH degradation appeared to be more frequent in both plant rhizospheres than in bulk sediment. In summary, this study suggests that halophyte plant colonization is an important driver of hydrocarbonoclastic bacterial community composition in estuarine environments, which can be exploited for in situ phytoremediation of OH in salt marsh environments.

Coral reefs around the globe have been subjected to a wide range of stressors. In the present study, fish species were recorded across a pronounced in-to-offshore gradient in the Jakarta Bay-Pulau Seribu reef system. In addition to this, fish species traits were obtained from FishBase. RLQ analysis revealed a significant association between fish species traits and environmental variables. Fish species associated with perturbed, inshore waters were resilient to disturbance, had higher mortality rates, higher growth rates and mainly consumed animals. In contrast, fish species associated with less perturbed, mid- and offshore waters had greater life expectancy, higher age at maturity, greater life span, greater generation time and mainly fed on plants or plants and animals. Eutrophication, pollution and physical destruction of coral substrate in inshore waters has thus selected for a low biomass and depauperate fish community characterised by fast growing and short lived species.

We compared the species composition, abundance, and cover of sponges in 2 marine lakes (Kakaban Lake and Haji Buang Lake) and adjacent coastal mangroves on the islands of Kakaban and Maratua in the Berau region of Indonesia. We recorded a total of 115 sponge spe- cies, 33 of which were restricted to Kakaban Lake, 18 to Haji Buang Lake, and 30 to coastal man- groves on Maratua Island. Only 13 species were shared among all habitats. The 2 marine lakes are located 10 km apart, but their assemblages were more similar to each other than to the bay man- grove systems just 200 to 500 m away. Our results show that marine lakes represent a distinct habitat with significantly higher sponge cover and abundance as well as a markedly different spe- cies composition when compared with coastal mangroves. In both lake and coastal mangrove habitats there was a pronounced gradient in composition away from the shore with the primary difference between solid (root or rock) and soft substrate (mud or sand). Each substrate type har- bored different sets of species in both lake and coastal mangrove habitats. There was no signifi- cant difference in sponge species composition, abundance, or cover between semi-permanent transects sampled in 2008 and 2009. We show for the first time that mangroves in the Indo-Pacific harbor a diverse array of sponge species and, further, that marine lakes harbor numerous unique species hitherto unknown to science. Bahruddin, Estradivari, N. Santo domingo, E. Dondorp, and W. Renema were invaluable sources of information and help in the field. We also thank the following people for their help in various ways: B. Hoeksema, Suharsono, Y. Tuti, E. Oberhauser, R. Suhr, and the staff of TNC/World Wildlife Foundation (WWF) Berau Office, Nabucco Island Dive Resort, and of Derawan Dive Resort. This study is part of a PhD project (L.E.B.) funded by NWO, division Earth and Life Sciences (ALW IPJ-07002; # 817.01.008). Fieldwork in Indonesia was made possible through additional financial support of WWF NetherlandsINNO Fund, the Schure-Beijerinck-Popping Fund of the Royal Dutch Academy of Science (KNAW), the TreubMaatschappij Fund, The Netherlands WWF-INNO Subsidy, the Leiden University Fund (LUF)/Slingelands, Singapore Airlines, the A.M. Buitendijk Fund and the J.J. ter Pelkwijk Fund (NCB Naturalis). D.F.R.C. was supported by the Portuguese Foundation for Science and Technology, FCT, project LESS CORAL, PTDC/AAC-AMB/115304/2009. We are grateful to the Indonesian Institute of Sciences (LIPI) and the Indonesian State Ministry of Research and Technology (RISTEK) for providing re search permits in Indonesia. R. van Soest, B. Hoeksema, and 4 anonymous reviewers provided valuable comments on the original manuscript. published

The present study aimed to assess if ragworm fatty acids (FA) profiles could be used to discriminate their spatial distribution in an historically mercury-contaminated estuarine environment, i.e., if it was possible to differentiate ragworms present in salt marsh sediments surrounding plant roots and rhizomes (rhizosediment) from adjacent unvegetated sediment. Additionally, we also tried to determine if ragworms differed in mercury content and if these values could also be used to identify the habitat they occur in. Results show that, within the same area, ragworms can be distinguished using FA profiles and that in halophyte rhizosediment ragworms display more than twice the levels of alpha-linolenic acid (18:3n-3). The ratio cis-vaccenic/oleic acids (18:1n-7/18:ln-9) in ragworms suggests higher carnivory in unvegetated sediments. Our study indicates that ragworm FA profiles can be used to identify their habitat, their trophic interaction with halophytes and reveal a spatially contrasting feeding behaviour, which also reflects mercury accumulation. published

We compare the environmental characteristics and bacterial communities associated with two rushes, Juncus maritimus and Bolboschoenus maritimus, and adjacent unvegetated habitat in a salt marsh subjected to historical mercury pollution. Mercury content was higher in vegetated than unvegetated habitat and increased with sampling depth. There was also a significant relationship between mercury concentration and bacterial composition. Habitat (Juncus, Bolboschoenus or unvegetated), sample depth, and the interaction between both, however, explained most of the variation in composition (∼70%). Variation in composition with depth was most prominent for the unvegetated habitat, followed by Juncus, but more constrained for Bolboschoenus habitat. This constraint may be indicative of a strong plant–microbe ecophysiological adaptation. Vegetated habitat contained distinct bacterial communities associated with higher potential activity of aminopeptidase, β-glucosidase and arylsulphatase and incorporation rates of 14C-glucose and 14C-acetate. Communities in unvegetated habitat were, in contrast, associated with both higher pH and proportion of sulphate reducing bacteria.

Coral reef ecosystems in Indonesia are among the most diverse in the world. Conserva- tion, restoration and management of marine biodiversity hotspots such as Indonesia's coral reefs require accurate baseline knowledge of the constituent species and the environmental conditions under which these species thrive. Here we present a study on the habitat structure and diversity, composition and abundance of reef sponges in the Derawan Islands, East Kalimantan, Indonesia. Mean live coral cover across depths and sites was just under 30%, while the mean cover of rubble and dead coral exceeded 40%. The distribution of live coral cover was patchy; the inshore sites had the lowest cover, while some offshore sites also had very low coral cover due to the effects of blast fishing. Rubble cover was highest inshore and beyond the barrier reef, whereas dead coral was most abundant in shallow-water and midshore reefs. A total of 168 sponge species or morphospecies were identified, of which Stelletta clavosa, Lamellodysidea herbacea, Niphates sp., Ircinia ramosa and Pet- rosia nigricans were the most common. Sponge composition varied in relation to distance from the Berau River and water visibility, in addition to sand cover and cover of encrusting corals. Importantly, sponges in the Derawan Islands appeared to thrive in inshore reefs that already had depauperate coral communities. This is in marked contrast to findings elsewhere in Indonesia (NW Java, SW Sulawesi) where inshore communities were depauperate for all taxa sampled.

In order to manage and conserve coral reefs it is essential to understand the factors that structure reef communities. In Indonesia’s Jakarta Bay – Pulau Seribu reef complex, pronounced on-to-offshore variation in a number of variables was observed. Live coral cover, and echinoderm and fish species richness were higher in midshore sites than either in- or offshore sites. Variation in habitat structure, the abiotic environment, distance between sample sites and covariation of these factors separately explained 9.6 to 15.1% of the spatial variation in the composition of corals, echinoderms and fishes. Together, all three components explained > 50% of the variation in composition. This indicates that spatial and environmental factors influence the distribution of species across the study area and have important implications for the large-scale management of this reef ecosystem. Large scalemanagement and protection of these reefs will probably be important because the majority or reefs were in poor to very poor condition as exemplified by low (

Very few coral reefs are located close enough to large cities to study the influence of large urban populations on reef assemblages. An exception is the Thousand Islands reef complex to the north of Jakarta, the capital city of Indonesia, and one of the largest conurbations in the world. Here we present data from a detailed survey where sponge assemblages were assessed at 30 patch reefs associated with islands in three coastal zones along an in-to-offshore gradient. Sponge assemblages are described at three taxonomic levels of detail (species, genus and family level). We recorded a total of 118 sponge species, 64 genera and 36 families, Aaptos suberitoides (Brønsted, 1934), Clathria (Thalysias) reinwardti (Vosmaer, 1880), Petrosia (Petrosia) nigricans (Lindgren, 1897) and Xestospongia testudinaria (Lamarck, 1813) were the most common species overall. There was a pronounced difference in composition among zones with the most distinct difference between the inshore zone and the other two zones. The inshore environment was characterised by very high turbidity and low live coral cover; the dominant substrate consisted of algal turf and sand. Environmental conditions improved and sponge diversity increased further offshore, although most areas appeared to have been affected by some form of disturbance. Ordinations were also largely congruent, at species, generic and family levels of taxonomic resolution. This indicates that variation in composition at higher taxonomic levels is a good indicator of variation at lower taxonomic levels, at least when there is a pronounced environmental gradient.

Very few coral reefs are located close enough to metropolitan cities to study the influence of large urban populations on reef communities. Here, we compare the impact of a large-scale disturbance gradient with local-scale disturbance on coral richness, cover, and composition in the Jakarta Bay and Pulau Seribu reef complex off Jakarta, Indonesia. We found no effect of local land-use type of coral reef islands on richness, composition or cover, nor did taxon richness differ among zones at the large-scale. There was, however, a pronounced difference in composition and coral cover among zones. Cover was very low and composition differed markedly in the near-shore zone 1 (Jakarta Bay) where human-induced disturbance is most intense. Cover was highest in the outlying reefs of zone 3. The highly perturbed zone 1 reefs were, furthermore, distinguished by the virtual absence of otherwise abundant coral taxa such as Acropora hyacinthus and Porites rus and the prevalence of taxa such as Oulastrea crispata and Favia maxima. Almost 60% of the spatial variation in composition was related to variation in shelf depth and island size. The importance of shelf depth was related to the prevalence of a strong environmental gradient in reef depth, pollution, and mechanical reef disturbance and salinity from Jakarta Bay to the outlying reefs. Although there was a significant univariate relationship between spatial variation in composition and distance, this did not enter into the multivariate model, except when presence–absence data was used, indicating that environmental processes are the primary structuring forces in determining local coral assemblage composition across the Pulau Seribu complex.

Relatively little is known about spatial turnover of marine benthic taxa in the diverse reef environments of Indonesia and how this is structured by environmental conditions. In the present study the community similarity of sponges was related to environmental and spatial variables. In total, 150 sponge species (N=15,842) were sampled within the Spermonde Archipelago in the Makassar Strait, off south-west Sulawesi. Ordination revealed that sponges are primarily structured by a complex interaction between depth, exposure and on-to-offshore variation in environmental variables. Together, environmental and spatial variables explained 56.9% of the variation in similarity of which 10.9% was due to environmental variables alone, 2.6% due to spatial variables alone and 43.4% due to covariation of environmental and spatial variables. The large amount of variation explained by the spatially structured environmental component is due to a strong on-to-offshore gradient in a number of environmental variables including temperature, velocity, salinity and suspended sediment load. Ordination was also used to identify associations between species and environmental variables.

A key question in ecology is how biological traits of species determine their locations within an ecosystem. Identifying associations between species traits and environmental variables can help us to understand the causes of disturbance and predict whether species with given traits will persist under changing environmental conditions. To this end corals and environmental variables were sampled in 20 patch reefs of Pulau Seribu, located to the northwest of Jakarta, Indonesia. RLQ analysis, a multivariate ordination approach was subsequently used to relate species traits (colony shape, colony form, corallite size, reproductive mode and adaptive strategy) to environmental variables (e.g., heavy metal concentration in seawater and sediment, salinity, dissolved oxygen, and the cover of sand, dead coral, algae, sponges and soft corals). Using RLQ analysis, we identified environmental gradients associated with significant variation in species traits. Stress tolerant species with a massive morphology, meandroid shape and large corallites were associated with sites with a high abundance of algae and a relatively high concentration of potentially toxic heavy metals in seawater including Cu and Cd, whereas ruderal species and species with a branching morphology and very small corallites were linked to midshore sites. Competitively dominant species with a laminar or free-living morphology, phaceloid shape, very large corallites and brooding reproductive mode were linked to offshore sites with abundant Ca and Sr in the sediment and a high cover of Halimeda algae and sponges. Results of this study indicate that disturbance has differentially affected the marine environment of the Pulau Seribu system, which in turn interacts with coral species traits to determine local species composition.

It is essential to understand how spatial differences in community composition are re- lated to environmental variables in order to explain and predict patterns in biodiversity. We investi- gated spatial variation in the composition of foraminifera assemblages and assessed the degree to which this could be explained by environmental variables and/or the distance among sample sites. Together, environmental and spatial variables explained 33.5% of the spatial variation in assemblage structure, of which 25.7% was due to environmental variables alone, 2.8% due to spatial variables alone and 5.0% due to covariation of environmental and spatial variables. Associations between the distribution of foraminifera and environmental variables were significantly influenced by species traits. Dinoflagellate symbionts and an orbitoidal chamber arrangement were linked to exposed reefs and a hard substrate, whereas rhodophyte symbionts were linked to sheltered reefs and a sandy sub- strate. With respect to depth, a hyaline skeletal structure was most strongly associated with deep water, whereas dinoflagellate and rhodophyte symbionts, an orbitoidal chamber arrangement and an imperforate skeletal structure were most strongly associated with shallow water environments. The association with given environmental variables was less pronounced for other traits. Species with spines, for example, were usually restricted to hard-substrate environments, and species with a coin shape to shallow-water environments, but there were species that deviated strongly from this general trend. Results of this study highlight the importance of environment variables in structuring foramin- fera assemblages, and further identify traits that appear to influence how species respond to these conditions.

In the present study, we assessed the composition of Bacteria in four biotopes namely sediment, seawater and two sponge species (Stylissa massa and Xestospongia testudinaria) at four different reef sites in a coral reef ecosystem in West Java, Indonesia. In addition to this, we used a predictive metagenomic approach to estimate to what extent nitrogen metabolic pathways differed among bacterial communities from different biotopes. We observed marked differences in bacterial composition of the most abundant bacterial phyla, classes and orders among sponge species, water and sediment. Proteobacteria were by far the most abundant phylum in terms of both sequences and Operational Taxonomic Units (OTUs). Predicted counts for genes associated with the nitrogen metabolism suggested that several genes involved in the nitrogen cycle were enriched in sponge samples, including nosZ, nifD, nirK, norB and nrfA genes. Our data show that a combined barcoded pyrosequencing and predictive metagenomic approach can provide novel insights into the potential ecological functions of the microbial communities. Not only is this approach useful for our understanding of the vast microbial diversity found in sponges but also to understand the potential response of microbial communities to environmental change.

The forest fires induced by the El Niño Southern Oscillation (ENSO) in 1997-1998 resulted in the temporary extirpation of more than 100 lowland butterfly species at a forest site in Borneo. Species with more restricted ranges were less likely to recover over the following four years. Matched-pair analyses revealed that species with lower initial abundances, restricted geographic ranges, and more specialized larvae were less likely to return. Specialization differed predictably between the (more generalist) wide-range and (more specialized) restricted-range species in our data set, and both geographic range and level of specialization were important in multivariate models. These are the first observations directly linking extent of occurrence, ecological specialization, and observed recovery following local extirpation. If recovery time exceeds the frequency of disturbance, local extirpation can lead to local extinction. Given that ENSO-induced disturbances are increasing in frequency, in severity, and in geographic scale, these results suggest that specialist species with restricted geographic ranges could be at particularly high risk of global extinction.

We assess the differential impact of logging and ENSO (El Nino Southern Oscillation)induced disturbance on the relative butterfly abundance and species richness of range-restricted and widespread species within the island of Borneo. Relative abundance and species richness were assessed using rarefaction and species accumulation curves in unburned isolates surrounded by burned forest, the burned forest itself, and continuous forest unaffected by ENSO-induced disturbance in addition to logged and unlogged landscapes in unburned forest. The relative abundance of endemics was significantly higher in unlogged forest than logged forest and significantly higher in unburned forest than burned forest. Rarefied species richness of range categories was similar (Bornean endemics) or higher (other categories) in selectively logged than unlogged forest. In contrast, rarefied species richness of range-restricted species was highest in continuous forest, intermediate in unburned isolates, and lowest in burned forest. Only two individuals of a single Bornean endemic species were found in all the burned forest. Although species richness was higher in all range categories in continuous forest than in unburned isolates and in burned forest, the difference was most pronounced for range-restricted species. Logging and ENSO-induced fires thus have contrasting effects on range-restricted species. While both increase the relative abundance of widely distributed species at the expense of range-restricted species, only ENSO-induced disturbance lowers the rarefied number of restricted range species. Our research highlights the threat that severe ENSO events pose to geographically restricted classes of biodiversity.

Sponge assemblages were investigated in the Spermonde Archipelago, southwestern Sulawesi, Indonesia. In this study spatial patterns of sponge similarity among sites were significantly related to remotely sensed environmental variables, the degree of human settlement and depth, but not to the distance between sites. Both oviparous and viviparous species groups responded to similar environmental constraints, and differences in similarity were unrelated to the distance between sites. The degree of human settlement, however, was significantly related to variation in the composition of viviparous, but not oviparous species. Our results demonstrate, most importantly, the utility of remotely sensed data in predicting the spatial turnover of diverse species assemblages such as sponges. Secondly, they show that patterns of human settlement in the Spermonde Archipelago appear to be affecting patterns of sponge beta diversity. These results highlight the need to assess and protect marine areas in biodiversity hotspots such as Indonesia.

In order to preserve diversity it is essential to understand how assemblages change across space. Despite this fact, we still know very little about how marine diversity is spatially distributed, especially among lesser-studied invertebrate taxa. In the present study beta-diversity patterns of sea urchins, sponges, mushroom corals and larger foraminifera were assessed in the Spermonde Archipelago (Indonesia). Using ordinations we showed that the inshore zone ( 30 km offshore) all contained distinct assemblages of sponges and corals, while only foraminifera assemblages from the inshore (

Borneo contains a diverse rainforest butterfly community, but its forests are under threat from logging and ENSO- (El Nino Southern Oscillation) induced fires. Contrasts in butterfly assemblage structure were examined in nine 450 ha landscapes in logged forest, primary unburned continuous and isolated forest, and forest affected by surface fires during the 1997/98 ENSO event. Temporally the effect of the 1997/98 ENSO event was followed in a single burned landscape from 1997 to 2004. In total, 517 species were present in 190 sampling sites. There was a five-fold difference in species richness among landscapes, with highest richness in continuous landscapes and lowest richness in burned landscapes. Richness was also higher in logged forest than proximate unlogged forest. Temporally, species richness dropped dramatically from 1997 to 1998, but after-wards increased remaining, however, substantially lower than pre-ENSO (1997) sampling. Sites in burned landscapes were distinct from other sites in terms of vegetation structure with the slash-and-burn area the most dissimilar to other landscapes. There was much less structure among unburned landscapes. The pattern of butterfly community composition was similar to that of vegetation structure with the community from the slash-and-burn area the most distinct. However, there was much less overlap among sites from different landscapes. Temporally, 1998 possessed the most distinct assemblage when compared to assemblages from other years. The community composition was, however, slowly returning to a pre-disturbance composition. Variance in community composition explained by environmental and spatial factors differed substantially among landscapes. The spatial fraction was the only explanatory component in recently burned landscapes and a proximate small unburned isolate, but explained no variation in logged landscapes. The environmental fraction explained substantial amounts of variation in logged landscapes and the slash-and-burn area. When all landscapes were pooled high proportions of variation in butterfly community composition were explained by both geographic distance between sites and environmental variables. In contrast when only unburned landscapes were considered, most variation was explained by the geographic distance among them. Despite differences among landscapes there was a general pattern of relatively sharp decline in similarity at short distances that levels out over greater distances, a result that agrees with previous studies on other tropical species assemblages.

Fire-affected forests are becoming an increasingly important component of tropical landscapes. The impact of wildfires on rainforest communities is, however, poorly understood. In this study the density, species richness and community composition of seedlings, saplings, trees and butterflies were assessed in unburned and burned forest following the 1997/98 El Nino Southern Oscillation burn event in East Kalimantan, Indonesia. More than half a year after the fires, sapling and tree densities in the burned forest were only 2.5% and 38.8%, respectively, of those in adjacent unburned forest. Rarefied species richness and Shannon's H' were higher in unburned forest than burned forest for all groups but only significantly so for seedlings. There were no significant differences in evenness between unburned and burned forest. Matrix regression and Akaike's information criterion (AIC) revealed that the best explanatory models of similarity included both burning and the distance between sample plots indicating that both deterministic processes (related to burning) and dispersal driven stochastic processes structure post-disturbance rainforest assemblages. Burning though explained substantially more variation in seedling assemblage structure whereas distance was a more important explanatory variable for trees and butterflies. The results indicate that butterfly assemblages in burned forest were primarily derived from adjacent unburned rainforest, exceptions being species of grass-feeders such as Orsotriaena medus that are normally found in open, disturbed areas, whereas burned forest seedling assemblages were dominated by typical pioneer genera, such as various Macaranga species that were absent or rare in unburned forest. Tree assemblages in the burned forest were represented by a subset of fire-resistant species, such as Eusideroxylon zwageri and remnant dominant species from the unburned forest.

The aims of this study are to compare cross-shelf variation in diversity and community composition of four benthic taxa (sea urchins, sponges, corals and foraminifera) in the reefs of the Spermonde Archipelago, Indonesia, and relate this variation to cross-shelf environmental parameters, i.e. distance offshore, depth and exposure to oceanic currents. Rarefied species richness and Shannon's H ′ varied unimodally with the distance offshore and depth for all taxa (except sea urchins) and were highest at intermediate distances offshore and depths. There was no significant association between evenness and distance offshore. Evenness did, however, vary with depth and exposure. Overall, models using distance offshore, depth and exposure explained most of the variation in sponge and coral diversity but substantially less variation in foraminifera diversity. Variation in composition depended on distance offshore, depth and exposure although the relative importance of these variables differed among taxa. Depth was the most important parameter for sponges, corals and foraminifera but not for sea urchins. Sponge and coral assemblages differed markedly from in-to-off-shore but there was relatively little variation in foraminifera assemblages with most foraminifera species having broad cross-shelf distributions. Foraminifera assemblages on the contrary differed markedly between exposed and sheltered reef environments; species in exposed reef environments, for example, consisted of species with distinct strategies for coping with the increased hydrodynamic energy. In summary, this study shows that benthic taxa in the Spermonde are distributed along continuous gradients (in-to-off-shore and shallow-to-deep) in addition to occupying discrete habitats related to reef exposure.

A comprehensive understanding of variables associated with spatial differences in community composition is essential to explain and predict biodiversity over landscape scales. In this study, spatial patterns of bird diversity in Central Kalimantan, Indonesia, were examined and associated with local-scale (habitat structure and heterogeneity) and landscape-scale (logging, slope position and elevation) environmental variables. Within the study area (c. 196 km2) local habitat structure and heterogeneity varied considerably, largely due to logging. In total 9747 individuals of 177 bird species were recorded. Akaike's information criterion (AIC) revealed that the best explanatory models of bird community similarity and species richness included both local- and landscape-scale environmental variables. Important local-scale variables included liana abundance, fern cover, sapling density, tree density, dead wood abundance and tree architecture, while important landscape-scale variables were elevation, logging and slope position. Geographic distance between sampling sites was not significantly associated with spatial variation in either species richness or similarity. These results indicate that deterministic environmental processes, as opposed to dispersal-driven stochastic processes, primarily structure bird assemblages within the spatial scale of this study and confirm that highly variable local habitat measures can be effective means of predicting landscape-scale community patterns.

Landscape-scale studies of community traits such as species richness and community composition are sorely needed to explore the impact of large-scale disturbance events such as ENSO (El Niño Southern Oscillation)-induced burning and habitat isolation on rain-forest communities. Here we assess butterflies in continuous forest, in unburned isolates surrounded by burned forest and in burned forest, in addition to areas sampled before the most recent (1997/98) large-scale burn event in Borneo. Overall levels of species richness were significantly higher pre-ENSO and in continuous forest than in unburned isolates and burned forest. There was, however, some variation among butterfly families in these patterns, with no significant differences among habitats (continuous forest, isolates and burned forest) for the Hesperiidae and significant differences for the other butterfly families. Patterns of community composition showed that similarity was greater between distant continuous forest and isolates than between either of these and burned forest. Since the unburned isolates were surrounded by the burned forest this indicates that the habitat (burned or unburned) overrides geographical differences. Dominant species that contributed substantially to differences among habitats were often completely absent from either burned or unburned forest. The combined patterns of species richness and community structure suggest that burning affects forest ecosystems by a replacement of dominant species while habitat isolation may affect areas by leading to the local extinction of rare species.

Aims Throughout South-East Asia, droughts associated with ENSO (El Nino Southern Oscillation) events have resulted in large-scale fires affecting millions of hectares of rain forest. However, the long-term impacts of these fires on the rain forest faunas are only poorly understood. Our aim was to study the recovery of rain forest butterfly assemblages following the 1997–98 ENSO event, which resulted in the largest-scale fires in the recorded history of the region. Location A 420-km2 area in the Balikpapan-Samarinda region of East Kalimantan, Indonesian Borneo. Methods Four landscapes were assessed after the 1997–98 ENSO event, including one landscape that was assessed prior to the event. Comparisons of species richness, species composition and guild abundance were made among landscapes and years. The relative importance of environment, geographical distance between sampling sites, and time between sampling years was quantified during the succession phase using a variance partitioning technique. Results The fires dramatically altered the butterfly community and resulted in a major decline in observed species richness within the landscape surveyed prior to the ENSO event. Following fires in 1998, butterfly assemblages in all landscapes were dominated by large-winged generalist species. During 1999 and 2000, assemblages became increasingly dominated by smaller specialist species. Species endemic to Borneo that were present before fires were absent in 2000, despite intensive sampling over enhanced spatial and environmental scales. Community similarity was significantly dependent upon local environmental variables, geographical distance between sampling sites, and time between sampling years. Together, these explained over 52% of the observed variation in samples. Conclusions The importance of geographical distance between sampling sites indicates that recovery was dependent upon colonization from proximate habitats. Despite an apparent trend of return to pre-ENSO community structure, low species richness throughout the survey area indicates that full recovery had not taken place by 2000.