Compositional analysis of bacterial communities in seawater, sediment, and sponges in the Misool coral reef system, Indonesia

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.publishe

Dynamics of Fungal Communities in Bulk and Maize Rhizosphere Soil in the Tropics

The fungal population dynamics in soil and in the rhizospheres of two maize cultivars grown in tropical soils were studied by a cultivation-independent analysis of directly extracted DNA to provide baseline data. Soil and rhizosphere samples were taken from six plots 20, 40, and 90 days after planting in two consecutive years. A 1.65-kb fragment of the 18S ribosomal DNA (rDNA) amplified from the total community DNA was analyzed by denaturing gradient gel electrophoresis (DGGE) and by cloning and sequencing. A rhizosphere effect was observed for fungal populations at all stages of plant development. In addition, pronounced changes in the composition of fungal communities during plant growth development were found by DGGE. Similar types of fingerprints were observed in two consecutive growth periods. No major differences were detected in the fungal patterns of the two cultivars. Direct cloning of 18S rDNA fragments amplified from soil or rhizosphere DNA resulted in 75 clones matching 12 dominant DGGE bands. The clones were characterized by their HinfI restriction patterns, and 39 different clones representing each group of restriction patterns were sequenced. The cloning and sequencing approach provided information on the phylogeny of dominant amplifiable fungal populations and allowed us to determine a number of fungal phylotypes that contribute to each of the dominant DGGE bands. Based on the sequence similarity of the 18S rDNA fragment with existing fungal isolates in the database, it was shown that the rhizospheres of young maize plants seemed to select the Ascomycetes order Pleosporales, while different members of the Ascomycetes and basidiomycetic yeast were detected in the rhizospheres of senescent maize plants

Heterotrophic activities of neustonic and planktonic bacterial communities in an estuarine environment (Ria de Aveiro)

The uppermost millimeter of the water column, the surface microlayer (SML), hosts bacterial communities (bacterioneuston) with potential metabolic adaptations to this unique physical and chemical environment. Hydrolysis and monomer incorporation by bacterioneuston and bacterioplankton communities in the estuarine system, Ria de Aveiro, was investigated and compared during a 2-year survey. The study was conducted at two contrasting sites, typifying the marine and brackish water characteristics of the estuary and with different sources, amounts and composition of organic matter. In the marine zone, bacterioneuston showed higher rates of hydrolysis and lower rates of monomer incorporation than bacterioplankton, whereas in the brackish water zone, neustonic and planktonic microbial communities showed similar activity rates. This pattern may result from the different degree of surface organic and inorganic matter enrichments, which reflect site-specific characteristics, such as hydrodynamics and sources of organic matter composition. In general, the estuarine SML environment favors polymer hydrolysis, but inhibits monomer utilization, in comparison with the subsurface layers. However, the differences between the two communities tend to decrease as autotrophic and heterotrophic activities increase in the brackish-water area

Diversity of ndo Genes in Mangrove Sediments Exposed to Different Sources of Polycyclic Aromatic Hydrocarbon Pollution▿

Polycyclic aromatic hydrocarbon (PAH) pollutants originating from oil spills and wood and fuel combustion are pollutants which are among the major threats to mangrove ecosystems. In this study, the composition and relative abundance in the sediment bacterial communities of naphthalene dioxygenase (ndo) genes which are important for bacterial adaptation to environmental PAH contamination were investigated. Three urban mangrove sites which had characteristic compositions and levels of PAH compounds in the sediments were selected. The diversity and relative abundance of ndo genes in total community DNA were assessed by a newly developed ndo denaturing gradient gel electrophoresis (DGGE) approach and by PCR amplification with primers targeting ndo genes with subsequent Southern blot hybridization analyses. Bacterial populations inhabiting sediments of urban mangroves under the impact of different sources of PAH contamination harbor distinct ndo genotypes. Sequencing of cloned ndo amplicons comigrating with dominant DGGE bands revealed new ndo genotypes. PCR-Southern blot analysis and ndo DGGE showed that the frequently studied nah and phn genotypes were not detected as dominant ndo types in the mangrove sediments. However, ndo genotypes related to nagAc-like genes were detected, but only in oil-contaminated mangrove sediments. The long-term impact of PAH contamination, together with the specific environmental conditions at each site, may have affected the abundance and diversity of ndo genes in sediments of urban mangroves

Relation between bacterial activity in the surface microlayer and estuarine hydrodynamics

Bacterial communities of the surface microlayer (SML) of the estuary Ria de Aveiro (Portugal) were characterized in terms of abundance and activity during a 2-year survey at two sites with distinct hydrodynamic properties (marine and brackish water zones). The hydrodynamic conditions were simulated using a bidimensional numerical model and related to the microbiological observations. The pattern of variation of bacterial biomass productivity (BBP) was distinct between the two sampling sites. At the outer site, BBP was significantly lower at the SML, whereas at the inner site, it was significantly enhanced at the SML. Although the total bacterial abundance was similar in the SML and underlying water (UW), the fraction of cells attached to particles was significantly higher at the SML (two to three times). The integration of microbiological results with environmental and hydrological variables shows that strong currents in the marine zone promote the vertical mixing, inhibiting the establishment of an SML bacterial community distinct from that of UW. In contrast, in the brackish water zone, lower current velocities provide conditions for enhancing the bacterial activity in the enriched SML. Estuarine dynamics influence the distribution and activity of microorganisms at the SML and in the water column, with anticipated impacts for the carbon cycle in the estuarine environment

Impact of freshwater inflow on bacterial abundance and activity in the estuarine system Ria de Aveiro

The influence of freshwater flow on bacterial communities in the estuarine system Ria de Aveiro (Portugal) was investigated at two sites differently impacted by river inputs, representative of the marine and brackish water zones of the estuary. Sampling events were clustered based on hydrological features. The hydrodynamic was simulated with a Lagrangian model and related to microbiological parameters. Estuarine bacteria responded to different freshwater regimes developing distinct patterns of abundance and activity at the marine and brackish water zones. A circulation pattern induced by high river inflow produced vertical stratification in the marine zone, promoting a seaward flux of bacterioplankton, and stimulating the import of riverine phytoplankton and particle-attached bacteria to the brackish water zone. Advective transport and resuspension processes contributed to a 3-times increase in abundance of particle-attached bacteria during intense freshwater inputs. Additionally, bacterial activity in the estuary was controlled by inorganic nitrogen, responding to different freshwater inputs, which, in association with different prevailing sources of organic substrates induced significant changes in bacterial production. The dynamic and main controlling factors of bacterial communities are clearly impacted by freshwater inputs. Therefore, significant changes in the recycling of nutrients by microbial activities can be expected from alterations in freshwater inputs either related to global climate change or regional hydrological regimes