Oxidation of As(III) by the Bacterial Community of a Marine Sediment Monitored by Microcalorimetry

Oxidation of arsenic(III) by the bacterial community of a contaminated sediment (from the Estaque marina, Marseille, France) was studied using microcalorimetry. A low, but reproducible, heat output was detectable during microbial As(III) oxidation. The heat produced was of the same order of magnitude as the heat value calculated from the standard molar enthalpy change for the As(III) oxidation by oxygen. Parameters associated with the biogeochemical cycles of arsenic, iron and carbon were studied in parallel. Amendment with arsenite delayed CO₂ production and increased the rate of Fe(II) oxidation in the sediment. These results suggest a correlation between arsenic and iron biogeochemical cycles and mineralization of organic matter.

Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the supplemental file.     

Effects of Three Polycyclic Aromatic Hydrocarbons on Sediment Bacterial Community

Mangrove sediment is susceptible to anthropogenic pollutants, including polycyclic aromatic hydrocarbons (PAHs). However, the effects of PAHs on the bacterial diversity in mangrove sediment have been rarely studied. In the present study, the effects of three types of PAHs (Naphthalene, Fluorene, and Pyrene) at three doses on sediment microbial populations were investigated by using denaturing gradient gel electrophoresis (DGGE). After 7 and 24 days of incubation of the three types of PAHs, markedly different patterns were observed in the bacterial communities. Overall, the diversity of bacterial community was suppressed before 7 days but was promoted after 24 days. Multidimensional scaling analysis suggested that the composition of bacterial communities after 7 days was distinctly distant from that after 24 days. Also despite a slight shift of bacterial abundance, the bacterial communities were relatively steady in these sediments after exposure to PAHs. In addition, DGGE suggested that the applications of three PAHs (especially PYR) had considerable effects on bacterial communities. For phylogenetic analysis, bacteria species belonging to Proteobacteria (α-, β-, and γ-), Actinobacteria, Chloroflexi, Bacteroidetes, and Planctomycetes were changed dramatically after treatment with PAHs. These results suggest that PAHs play key roles in the change of bacterial community, which may be important for understanding the relationship between PAHs and sediment microbial ecology.     

Methylation of Mercury in Earthworms and the Effect of Mercury on the Associated Bacterial Communities

Methylmercury compounds are very toxic for most organisms. Here, we investigated the potential of earthworms to methylate inorganic-Hg. We hypothesized that the anaerobic and nutrient-rich conditions in the digestive tracts of earthworm''s promote the methylation of Hg through the action of their gut bacteria. Earthworms were either grown in sterile soils treated with an inorganic (HgCl₂) or organic (CH₃HgCl) Hg source, or were left untreated. After 30 days of incubation, the total-Hg and methyl-Hg concentrations in the soils, earthworms, and their casts were analyzed. The impact of Hg on the bacterial community compositions in earthworms was also studied. Tissue concentrations of methyl-Hg in earthworms grown in soils treated with inorganic-Hg were about six times higher than in earthworms grown in soils without Hg. Concentrations of methyl-Hg in the soils and earthworm casts remained at significantly lower levels suggesting that Hg was mainly methylated in the earthworms. Bacterial communities in earthworms were mostly affected by methyl-Hg treatment. Terminal-restriction fragments (T-RFs) affiliated to Firmicutes were sensitive to inorganic and methyl-Hg, whereas T-RFs related to Betaproteobacteria were tolerant to the Hg treatments. Sulphate-reducing bacteria were detected in earthworms but not in soils.     

Impacts of Cultivation of Marine Diatoms on the Associated Bacterial Community

The composition of bacterial communities associated with four diatom species was monitored during isolation and cultivation of algal cells. Strong shifts in the associated communities, linked with an increase in the numbers of phylotypes belonging to members of the Gammaproteobacteria, were observed during cultivation.     

Fluid and Sediment Dynamic Effects on Marine Benthic Community Structure

Fluid and sediment dynamics affect benthic community dynamicsand structure in manifold ways. We single out three community-structuringprocesses that are both strongly affected and amenable to controlledmanipulation: microbial population growth, faunal recruitment,and particle feeding. Attachment and colony growth rates ofmicrobes depend on the details of near-bed fluid exchange. Theiremigration and colony growth rates are affected by erosion ofmicrobial filmsand by abrasion during sediment transport. Recruitment and successional patterns of metazoans, especiallythose resulting from the settlement of weakly swimming, smalllarvae and juveniles, also are very sensitive to local variationsin boundary layer flow pattern and strength. While the importanceof particle fluxes to suspension feeders has long been apparent,the foraging patterns of a growing number of surface depositfeeders are being found to reflect a dependence upon sedimenttransport. Although these three processes have spatial and temporalscales amenable to both laboratory and field experimentation,proper dynamic scaling of laboratory model flows may not alwaysbe easy. Even the simplest two-phase (particles plus liquids,where particles can be bacteria, floes, larvae, or sediments)flows must match appropriate laboratory and field Reynolds number,Froude number, particle-fluid density (weight per unit volume)ratio, and the ratio of boundary layer thickness to particlesize, if the laboratory flow model is to provide accurate results.     

连作对麦冬根际土壤细菌群落的影响

以中草药麦冬为研究对象,采用变性梯度凝胶电泳(DGGE)方法,考察连作对麦冬根际土壤细菌群落的影响。结果表明,重茬麦冬根际细菌群落的Shannon-Wiener指数从苗期至快速生长期、再到块根膨大期分别为3.36-3.40-3.69,丰富度指数为55.0-61.5-63.5,均匀度指数为0.84-0.82-0.89;而同期正茬根际细菌群落的上述指数值分别为3.66-3.33-3.72、67.5-53.5-63.5和0.87-0.84-0.90。通过对土壤细菌群落的DGGE图谱进行主成分分析,结果显示,上述各个时期重茬与正茬样本均发生显著分离,表明连作改变了麦冬根际细菌群落的多样性变化趋势和结构组成。进一步比较麦冬块根膨大期根际主要功能菌群的数量变化,发现连作后氨化细菌和好气性纤维素分解菌数量增加,而硝化细菌和固氮菌的数量减少。对比发现重茬麦冬的产量仅为正茬的70.6%,表明麦冬连作减产与其根际土壤细菌群落的变化相关。     

The Gut Bacterial Community of Mammals from Marine and Terrestrial Habitats

After birth, mammals acquire a community of bacteria in their gastro-intestinal tract, which harvests energy and provides nutrients for the host. Comparative studies of numerous terrestrial mammal hosts have identified host phylogeny, diet and gut morphology as primary drivers of the gut bacterial community composition. To date, marine mammals have been excluded from these comparative studies, yet they represent distinct examples of evolutionary history, diet and lifestyle traits. To provide an updated understanding of the gut bacterial community of mammals, we compared bacterial 16S rRNA gene sequence data generated from faecal material of 151 marine and terrestrial mammal hosts. This included 42 hosts from a marine habitat. When compared to terrestrial mammals, marine mammals clustered separately and displayed a significantly greater average relative abundance of the phylum Fusobacteria. The marine carnivores (Antarctic and Arctic seals) and the marine herbivore (dugong) possessed significantly richer gut bacterial community than terrestrial carnivores and terrestrial herbivores, respectively. This suggests that evolutionary history and dietary items specific to the marine environment may have resulted in a gut bacterial community distinct to that identified in terrestrial mammals. Finally we hypothesize that reduced marine trophic webs, whereby marine carnivores (and herbivores) feed directly on lower trophic levels, may expose this group to high levels of secondary metabolites and influence gut microbial community richness.     

Shallow Water Marine Sediment Bacterial Community Shifts Along a Natural CO2 Gradient in the Mediterranean Sea Off Vulcano,Italy

The effects of increasing atmospheric CO₂ on ocean ecosystems are a major environmental concern, as rapid shoaling of the carbonate saturation horizon is exposing vast areas of marine sediments to corrosive waters worldwide. Natural CO₂ gradients off Vulcano, Italy, have revealed profound ecosystem changes along rocky shore habitats as carbonate saturation levels decrease, but no investigations have yet been made of the sedimentary habitat. Here, we sampled the upper 2 cm of volcanic sand in three zones, ambient (median pCO₂ 419 μatm, minimum Ω_arag 3.77), moderately CO₂-enriched (median pCO₂ 592 μatm, minimum Ω_arag 2.96), and highly CO₂-enriched (median pCO₂ 1611 μatm, minimum Ω_arag 0.35). We tested the hypothesis that increasing levels of seawater pCO₂ would cause significant shifts in sediment bacterial community composition, as shown recently in epilithic biofilms at the study site. In this study, 454 pyrosequencing of the V1 to V3 region of the 16S rRNA gene revealed a shift in community composition with increasing pCO₂. The relative abundances of most of the dominant genera were unaffected by the pCO₂ gradient, although there were significant differences for some 5 % of the genera present (viz. Georgenia, Lutibacter, Photobacterium, Acinetobacter, and Paenibacillus), and Shannon Diversity was greatest in sediments subject to long-term acidification (>100 years). Overall, this supports the view that globally increased ocean pCO₂ will be associated with changes in sediment bacterial community composition but that most of these organisms are resilient. However, further work is required to assess whether these results apply to other types of coastal sediments and whether the changes in relative abundance of bacterial taxa that we observed can significantly alter the biogeochemical functions of marine sediments.     

Biogeography of the Sediment Bacterial Community Responds to a Nitrogen Pollution Gradient in the East China Sea

Patterns of microbial distribution represent the integrated effects of historical and biological processes and are thus a central issue in ecology. However, there is still active debate on whether dispersal limitation contributes to microbial diversification in strongly connected systems. In this study, sediment samples were collected along a transect representing a variety of seawater pollution levels in the East China Sea. We investigated whether changes in sediment bacterial community structures would indicate the effects of the pollution gradient and of dispersal limitation. Our results showed consistent shifts in bacterial communities in response to pollution. More geographically distant sites had more dissimilar communities (r = −0.886, P < 0.001) in this strongly connected sediment ecosystem. A variance analysis based on partitioning by principal coordinates of neighbor matrices (PCNM) showed that spatial distance (dispersal limitation) contributed more to bacterial community variation (8.2%) than any other factor, although the environmental factors explained more variance when combined (11.2%). In addition, potential indicator taxa (primarily affiliated with Deltaproteobacteria and Gammaproteobacteria) were identified; these taxa characterized the pollution gradient. This study provides direct evidence that dispersal limitation exists in a strongly connected marine sediment ecosystem and that candidate indicator taxa can be applied to evaluate coastal pollution levels.     

Sediment Microbial Community Structure and Mercury Methylation in Mercury-Polluted Clear Lake, California

Spatial and temporal variations in sediment microbial community structure in a eutrophic lake polluted with inorganic mercury were identified using polar lipid fatty acid (PLFA) analysis. Microbial community structure was strongly related to mercury methylation potential, sediment organic carbon content, and lake location. Pore water sulfate, total mercury concentrations, and organic matter C/N ratios showed no relationships with microbial community structure. Seasonal changes and changes potentially attributable to temperature regulation of bacterial membranes were detectable but were less important influences on sediment PLFA composition than were differences due to lake sampling location. Analysis of biomarker PLFAs characteristic of Desulfobacter and Desulfovibrio groups of sulfate-reducing bacteria suggests that Desulfobacter-like organisms are important mercury methylators in the sediments, especially in the Lower Arm of Clear Lake.     

Survey of Motile Microaerophilic Bacterial Morphotypes in the Oxygen Gradient above a Marine Sulfidic Sediment

Enrichment cultures for free-swimming microaerophilic bacteria were prepared from marine sulfidic sediment samples (Nivå Bay, Denmark). We observed nine different morphotypes; three of these morphotypes represented already-described species, i.e., Thiovulum majus, “Candidatus Ovobacter propellens,” and an as-yet-unnamed large vibrioid bacterium. In addition, we observed several morphotypes of spirilla and one vibrioid morphotype. A common feature of all investigated bacteria was that they aggregated chemotactically at the oxic-anoxic interface, whereas preferred oxygen concentration were in the range of 1 to 10 μM. The motile behavior and flagellar dynamics are analyzed in detail with an emphasis on spirilla.     

Changes in Sediment Bacterial Community in Response to Long-Term Nutrient Enrichment in a Subtropical Seagrass-Dominated Estuary

Florida Bay exhibits a natural gradient of strong P limitation in the east which shifts to weak P or even N limitation at the western boundary. This nutrient gradient greatly affects seagrass abundance and productivity across the bay. We assessed the effects of N and P additions on sediment bacterial community structure in relation to the existing nutrient gradient in Florida Bay. Sediment samples from 24 permanent 0.25 m² plots in each of six sites across Florida Bay were fertilized with granular N and P in a factorial design for 26 months. Sediment bacterial community structure was analyzed using PCR-denaturing gradient gel electrophoresis (DGGE) analysis of 16S ribosomal RNA (rRNA) genes and a cloning strategy from DGGE bands. The phylogenetic positions of 16S rRNA sequences mostly fell into common members found in marine sediments such as sulfate-reducing Deltaproteobacteria, Gammaproteobacteria, Spirochaetes, and Bacteriodetes. Twenty-eight common DGGE bands were found in all sediment samples; however, some DGGE bands were only found or were better represented in eastern sites. Bacterial community diversity (Shannon-Weiner index) showed similar values throughout all sediment samples. The N treatment had no effect on the bacterial community structures across the bay. Conversely, the addition of P significantly influenced the bacterial community structure at all but the most western site, where P is least limiting due to inputs from the Gulf of Mexico. P additions enhanced DGGE band sequences related to Cytophagales, Ectothiorhodospiraceae, and Desulfobulbaceae, suggesting a shift toward bacterial communities with increased capability to degrade polymeric organic matter. In addition, a band related to Deferribacteres was enhanced in eastern sites. Thus, indigenous environmental conditions were the primary determining factors controlling the bacterial communities, while the addition of P was a secondary determining factor. This P-induced change in community composition tended to be proportional to the amount of P limitation obviated by the nutrient additions.     

Mercury Exposure: Protein Biomarkers of Mercury Exposure in Jaraqui Fish from the Amazon Region

Poly-trans-[(2-carboxyethyl)germasesquioxane] (Ge-132) is a water-soluble organogermanium compound that exerts various physiological effects, including anti-inflammatory activity and pain relief. In water, Ge-132 is hydrolyzed to 3-(trihydroxygermyl)propanoic acid (THGP), which in turn is capable of interacting with cis-diol compounds through its trihydroxy group, indicating that this compound could also interact with diol-containing nucleic acid constituents. In this study, we evaluated the ability of THGP to interact with nucleosides or nucleotides via nuclear magnetic resonance (NMR) analysis. In addition, we evaluated the effect of added THGP on the enzymatic activity of adenosine deaminase (ADA) when using adenosine or 2′-deoxyadenosine as a substrate. In solution, THGP indeed formed complexes with nucleotides or nucleosides through their cis-diol group. Moreover, the ability of THGP to form complexes with nucleotides was influenced by the number of phosphate groups present on the ribose moiety. Notably, THGP also inhibited the catalysis of adenosine by ADA in a concentration-dependent manner. Thus, interactions between THGP and important biological nucleic acid constituents might be implicated in the physiological effects of Ge-132.     

The Effect of Antibiotics on Associated Bacterial Community of Stored Product Mites

Background

Bacteria are associated with the gut, fat bodies and reproductive organs of stored product mites (Acari: Astigmata). The mites are pests due to the production of allergens. Addition of antibiotics to diets can help to characterize the association between mites and bacteria.

Methodology and Principal Findings

Ampicillin, neomycin and streptomycin were added to the diets of mites and the effects on mite population growth (Acarus siro, Lepidoglyphus destructor and Tyrophagus putrescentiae) and associated bacterial community structure were assessed. Mites were treated by antibiotic supplementation (1 mgg⁻¹ of diet) for 21 days and numbers of mites and bacterial communities were analyzed and compared to the untreated control. Bacterial quantities, determined by real-time PCR, significantly decreased in antibiotic treated specimens from 5 to 30 times in A. siro and T. putrescentiae, while no decline was observed in L. destructor. Streptomycin treatment eliminated Bartonella-like bacteria in the both A. siro and T. putrescentiae and Cardinium in T. putrescentiae. Solitalea-like bacteria proportion increased in the communities of neomycin and streptomycin treated A. siro specimens. Kocuria proportion increased in the bacterial communities of ampicillin and streptomycin treated A. siro and neomycin and streptomycin treated L. destructor.

Conclusions/Significance

The work demonstrated the changes of mite associated bacterial community under antibiotic pressure in pests of medical importance. Pre-treatment of mites by 1 mgg⁻¹ antibiotic diets improved mite fitness as indicated accelerated population growth of A. siro pretreated streptomycin and neomycin and L. destructor pretreated by neomycin. All tested antibiotics supplemented to diets caused the decrease of mite growth rate in comparison to the control diet.     

The Effect of Stable Dissolved-Oxygen Stress on Marine Benthic Invertebrate Community Diversity

The Fosa de Cariaco off the coast of Venezuela is an anoxic basin which is subject to small seasonal fluctuations in the depth of the anoxic water. Samples taken in the interface region (between oxic and anoxic waters) contained from 13 to 37 species represented by 117 to 380 individuals. Species-diversity, based on H′(s), was greater than that previously reported for samples from oxygen minimum regions. It is suggested that the relatively stable low dissolvedoxygen concentrations allow the development of diverse assemblages.     

Links between Phytoplankton and Bacterial Community Dynamics in a Coastal Marine Environment

Bacteria and phytoplankton dynamics are thought to be closely linked in coastal marine environments, with correlations frequently observed between bacterial and phytoplankton biomass. In contrast, little is known about how these communities interact with each other at the species composition level. The purpose of the current study was to analyze bacterial community dynamics in a productive, coastal ecosystem and to determine whether they were related to phytoplankton community dynamics. Near-surface seawater samples were collected in February, May, July, and September 2000 from several stations in the Bay of Fundy. Savin et al. (M.C. Savin et al., Microb Ecol 48: 51-65) analyzed the phytoplankton community in simultaneously collected samples. The attached and free-living bacterial communities were collected by successive filtration onto 5 m and 0.22 m pore-size filters, respectively. DNA was extracted from filters and bacterial 16S rRNA gene fragments were amplified and analyzed by denaturing gradient gel electrophoresis (DGGE). DGGE revealed that diversity and temporal variability were lower in the free-living than the attached bacterial community. Both attached and free-living communities were dominated by members of the Roseobacter and Cytophaga groups. Correspondence analysis (CA) ordination diagrams showed similar patterns for the phytoplankton and attached bacterial communities, indicating that shifts in the species composition of these communities were linked. Similarly, canonical CA revealed that the diversity, abundance, and percentage of diatoms in the phytoplankton community accounted for a significant amount of the variability in the attached bacterial community composition. In contrast, ordination analyses did not reveal an association between free-living bacteria and phytoplankton. These results suggest that there are specific interactions between phytoplankton and the bacteria attached to them, and that these interactions influence the composition of both communities.