Community Structure of Filamentous, Sheath-Building Sulfur Bacteria, Thioploca spp., off the Coast of Chile

The filamentous sulfur bacteria Thioploca spp. produce dense bacterial mats in the shelf area off the coast of Chile and Peru. The mat consists of common sheaths, shared by many filaments, that reach 5 to 10 cm down into the sediment. The structure of the Thioploca communities off the Bay of Concepcion was investigated with respect to biomass, species distribution, and three-dimensional orientation of the sheaths. Thioploca sheaths and filaments were found across the whole shelf area within the oxygen minimum zone. The maximum wet weight of sheaths, 800 g m(sup-2), was found at a depth of 90 m. The bacterial filaments within the sheaths contributed about 10% of this weight. The highest density of filaments was found within the uppermost 1 cm of the mat. On the basis of diameter classes, it was possible to distinguish populations containing only Thioploca spp. from mixed populations containing Beggiatoa spp. Three distinct size classes of Thioploca spp. were found, two of which have been described previously as Thioploca araucae and Thioploca chileae. Many Thioploca filaments did not possess a visible sheath, and about 20% of the sheaths contained more than one Thioploca species. The three-dimensional sheath structure showed that Thioploca filaments can move from the surface and deep into the sediment.     

Bacteria Associated with the Gills of Salmonid Fishes in Freshwater

The bacteria on the gills of 7 species of freshwater salmonid fishes were examined qualitatively and quantitatively. Both wild and hatchery cultured salmonids were examined. The former were obtained from 12 different locations in British Columbia. Species of Pseudomonas and Cytophaga predominated on both groups of fish. The microflora of the wild fish also contained Aeromonas and members of the Brevibacterium –coryneform– Erysipelothrix group. The microflora of cultured fish was less varied. As many as 10⁶ viable organisms/g wet weight of gill tissue were recovered.     

Morphological and Phylogenetic Characterizations of Freshwater Thioploca Species from Lake Biwa, Japan, and Lake Constance, Germany

Filamentous, gliding, sulfide-oxidizing bacteria of the genus Thioploca were found on sediments in profundal areas of Lake Biwa, a Japanese freshwater mesotrophic lake, and were characterized morphologically and phylogenetically. The Lake Biwa Thioploca resembled morphologically Thioploca ingrica, a brackish water species from a Danish fjord. The diameters of individual trichomes were 3 to 5.6 μm; the diameters of complete Thioploca filaments ranged from 18 to 75 μm. The cell lengths ranged from 1.2 to 3.8 μm. In transmission electron microscope specimens stained with uranyl acetate, dense intracellular particles were found, which did not show any positive signals for phosphorus and sulfur in an X-ray analysis. The 16S rRNA gene of the Thioploca from Lake Biwa was amplified by using newly designed Thioploca-specific primers (706-Thioploca, Biwa160F, and Biwa829R) in combination with general bacterial primers in order to avoid nonspecific amplification of contaminating bacterial DNA. Denaturing gradient gel electrophoresis (DGGE) analysis of the three overlapping PCR products resulted in single DGGE bands, indicating that a single 16S rRNA gene had been amplified. With the same method, the Thioploca from Lake Constance was examined. The 16S rRNA sequence was verified by performing fluorescence in situ hybridization targeted at specific motifs of the Lake Biwa Thioploca. Positive signals were obtained with the bacterial probe EUB-338, the γ-proteobacterial probe GAM42a, and probe Biwa829 targeting the Lake Biwa Thioploca. Based on the nearly complete 16S rRNA sequence and on morphological similarities, the Thioploca from Lake Biwa and the Thioploca from Lake Constance are closely related to T. ingrica and to each other.     

Carbon Monoxide Oxidation by Bacteria Associated with the Roots of Freshwater Macrophytes

The potential rates and control of aerobic root-associated carbon monoxide (CO) consumption were assessed by using excised plant roots from five common freshwater macrophytes. Kinetic analyses indicated that the maximum potential uptake velocities for CO consumption ranged from 0.4 to 2.7 μmol of CO g (dry weight)⁻¹ h⁻¹ for the five species. The observed rates were comparable to previously reported rates of root-associated methane uptake. The apparent half-saturation constants for CO consumption ranged from 50 to 370 nM CO; these values are considerably lower than the values obtained for methane uptake. The CO consumption rates reached maximum values at temperatures between 27 and 32°C, and there was a transition to CO production at ≥44°C, most likely as a result of thermochemical organic matter decomposition. Incubation of roots with organic substrates (e.g., 5 mM syringic acid, glucose, alanine, and acetate) dramatically reduced the rate of CO consumption, perhaps reflecting a shift in metabolism by facultative CO oxidizers. Based on responses to a suite of antibiotics, most of the CO consumption (about 90%) was due to eubacteria rather than fungi or other eucaryotes. Based on the results of acetylene inhibition experiments, methanotrophs and ammonia oxidizers were not active CO consumers.     

Ferric Iron Reduction by Bacteria Associated with the Roots of Freshwater and Marine Macrophytes

In vitro assays of washed, excised roots revealed maximum potential ferric iron reduction rates of >100 μmol g (dry weight)⁻¹ day⁻¹ for three freshwater macrophytes and rates between 15 and 83 μmol (dry weight)⁻¹ day⁻¹ for two marine species. The rates varied with root morphology but not consistently (fine root activity exceeded smooth root activity in some but not all cases). Sodium molybdate added at final concentrations of 0.2 to 20 mM did not inhibit iron reduction by roots of marine macrophytes (Spartina alterniflora and Zostera marina). Roots of a freshwater macrophyte, Sparganium eurycarpum, that were incubated with an analog of humic acid precursors, anthroquinone disulfate (AQDS), reduced freshly precipitated iron oxyhydroxide contained in dialysis bags that excluded solutes with molecular weights of >1,000; no reduction occurred in the absence of AQDS. Bacterial enrichment cultures and isolates from freshwater and marine roots used a variety of carbon and energy sources (e.g., acetate, ethanol, succinate, toluene, and yeast extract) and ferric oxyhydroxide, ferric citrate, uranate, and AQDS as terminal electron acceptors. The temperature optima for a freshwater isolate and a marine isolate were equivalent (approximately 32°C). However, iron reduction by the freshwater isolate decreased with increasing salinity, while reduction by the marine isolate displayed a relatively broad optimum salinity between 20 and 35 ppt. Our results suggest that by participating in an active iron cycle and perhaps by reducing humic acids, iron reducers in the rhizoplane of aquatic macrophytes limit organic availability to other heterotrophs (including methanogens) in the rhizosphere and bulk sediments.     

Community Structure of the Bacteria Associated with Nodularia sp. (Cyanobacteria) Aggregates in the Baltic Sea

The community structure of the bacteria associated with Nodularia spumigena (Mertens) cyanobacterial aggregates in the Baltic Sea was studied with temperature gradient gel electrophoresis (TGGE), using a 16S rRNA gene fragment as a target. Various developmental stages of the aggregates and free-floating cyanobacterial filaments were sampled to reveal possible changes in associated microbial community structure during development and senescence of the aggregates. The microbial community structures of all samples differed, and the communities of young and decaying aggregates were separated by cluster analysis of the TGGE fingerprint data. Sequencing of the TGGE fragments indicated the presence of bacteria from the α-, β-, and γ-proteobacterial groups, as well as members of Cytophaga–Flexibacter–Bacteroides lineages and gram-positive Actinobacteria spp. The majority of the Nodularia-associated sequences were not closely related to previously reported 16S rDNA sequences from the Baltic Sea or any other environment. The structure of the bacterial assemblage reflects the environmental changes associated with the succession and decay of the cyanobacterial aggregates. In addition, the sequence data suggest that the N. spumigena (Mertens) blooms in the Baltic Sea may host thus far uncharacterized bacterial species.     

Properties of Soil Pore Space Regulate Pathways of Plant Residue Decomposition and Community Structure of Associated Bacteria

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO₂ emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S–18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75–80% of the added plant residue was decomposed, cumulative CO₂ emission constituted 1,200 µm C g^-1 soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO₂ emission constituted 2,000 µm C g^-1 soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO₂ emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C decomposition processes.     

Plant Invasions Associated with Change in Root-Zone Microbial Community Structure and Diversity

The importance of plant-microbe associations for the invasion of plant species have not been often tested under field conditions. The research sought to determine patterns of change in microbial communities associated with the establishment of invasive plants with different taxonomic and phenetic traits. Three independent locations in Virginia, USA were selected. One site was invaded by a grass (Microstegium vimineum), another by a shrub (Rhamnus davurica), and the third by a tree (Ailanthus altissima). The native vegetation from these sites was used as reference. 16S rRNA and ITS regions were sequenced to study root-zone bacterial and fungal communities, respectively, in invaded and non-invaded samples and analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Though root-zone microbial community structure initially differed across locations, plant invasion shifted communities in similar ways. Indicator species analysis revealed that Operational Taxonomic Units (OTUs) closely related to Proteobacteria, Acidobacteria, Actinobacteria, and Ascomycota increased in abundance due to plant invasions. The Hyphomonadaceae family in the Rhodobacterales order and ammonia-oxidizing Nitrospirae phylum showed greater relative abundance in the invaded root-zone soils. Hyphomicrobiaceae, another bacterial family within the phyla Proteobacteria increased as a result of plant invasion, but the effect associated most strongly with root-zones of M. vimineum and R. davurica. Functional analysis using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) showed bacteria responsible for nitrogen cycling in soil increased in relative abundance in association with plant invasion. In agreement with phylogenetic and functional analyses, greater turnover of ammonium and nitrate was associated with plant invasion. Overall, bacterial and fungal communities changed congruently across plant invaders, and support the hypothesis that nitrogen cycling bacteria and functions are important factors in plant invasions. Whether the changes in microbial communities are driven by direct plant microbial interactions or a result of plant-driven changes in soil properties remains to be determined.     

A Cytochemical Study of Extracellular Sheaths Associated with Rigidoporus lignosus during Wood Decay

An ultrastructural and cytochemical investigation of the development of Rigidoporus lignosus, a white-rot fungus inoculated into wood blocks, was carried out to gain better insight into the structure and role of the extracellular sheaths produced by this fungus during wood degradation. Fungal sheaths had a dense or loose fibrillar appearance and were differentiated from the fungal cell wall early after wood inoculation. Close association between extracellular fibrils and wood cell walls was observed at both early and advanced stages of wood alteration. Fungal sheaths were often seen deep in host cell walls, sometimes enclosing residual wood fragments. Specific gold probes were used to investigate the chemical nature of R. lignosus sheaths. While labeling of chitin, pectin, β-1,4- and β-1,3-glucans, β-glucosides, galactosamine, mannose, sialic acid, RNA, fucose, and fimbrial proteins over fungal sheaths did not succeed, galactose residues and laccase (a fungal phenoloxidase) were found to be present. The positive reaction of sheaths with the PATAg test indicates that polysaccharides such as β-1,6-glucans are important components. Our data suggest that extracellular sheaths produced by R. lignosus during host cell colonization play an important role in wood degradation. Transportation of lignin-degrading enzymes by extracellular fibrils indicates that alteration of plant polymers may occur within fungal sheaths. It is also proposed that R. lignosus sheaths may be involved in recognition mechanisms in fungal cell-wood surface interactions.     

Bacterial Community Structure Associated with a Dimethylsulfoniopropionate-Producing North Atlantic Algal Bloom

The bacteria associated with oceanic algal blooms are acknowledged to play important roles in carbon, nitrogen, and sulfur cycling, yet little information is available on their identities or phylogenetic affiliations. Three culture-independent methods were used to characterize bacteria from a dimethylsulfoniopropionate (DMSP)-producing algal bloom in the North Atlantic. Group-specific 16S rRNA-targeted oligonucleotides, 16S ribosomal DNA (rDNA) clone libraries, and terminal restriction fragment length polymorphism analysis all indicated that the marine Roseobacter lineage was numerically important in the heterotrophic bacterial community, averaging >20% of the 16S rDNA sampled. Two other groups of heterotrophic bacteria, the SAR86 and SAR11 clades, were also shown by the three 16S rRNA-based methods to be abundant in the bloom community. In surface waters, the Roseobacter, SAR86, and SAR11 lineages together accounted for over 50% of the bacterial rDNA and showed little spatial variability in abundance despite variations in the dominant algal species. Depth profiles indicated that Roseobacter phylotype abundance decreased with depth and was positively correlated with chlorophyll a, DMSP, and total organic sulfur (dimethyl sulfide plus DMSP plus dimethyl sulfoxide) concentrations. Based on these data and previous physiological studies of cultured Roseobacter strains, we hypothesize that this lineage plays a role in cycling organic sulfur compounds produced within the bloom. Three other abundant bacterial phylotypes (representing a cyanobacterium and two members of the α Proteobacteria) were primarily associated with chlorophyll-rich surface waters of the bloom (0 to 50 m), while two others (representing Cytophagales and δ Proteobacteria) were primarily found in deeper waters (200 to 500 m).     

Influence of Species Specificity and Other Factors on Bacteria Associated with the Coral Stylophora pistillata in Taiwan

Species of bacteria associated with Stylophora pistillata were determined by analyses of 16S ribosomal genes. Coral samples were taken from two distinct sites at Kenting, in the far south of Taiwan; three coral colonies at each site were tagged and sampled in the winter and summer of 2007. Six hundred 16S rRNA gene clones were selected and sequenced for diversity analysis and community comparison. LIBSHUFF and nonparametric multiple dimensional scaling analyses showed variations in the composition of the coral-associated bacteria in the different samples, suggesting that seasonal and geographic factors and variations in individual coral colonies were all vital drivers of the structure of the S. pistillata-associated bacterial community. To examine the association between species specificity and environmental impacts on the structure of the coral-associated bacterial community, we conducted an integrated, comparative analysis of 44 coral-associated bacterial data sets, including the present study''s data. The clustering analysis suggests that the influence of spatial and temporal factors on the coral-associated bacteria population structure is considerable; nonetheless, the effect of species specificity is still detectable in some coral species, especially those from the Caribbean Sea.Microbes are abundant in the ocean and thrive around corals. In earlier investigations over the past decades, microbes have been detected in coral mucus (8), in coral tissues (5), and in the surrounding reef waters (25). Although we understand little about the real interactions between these coral-associated microbes and the coral itself, or their mutual roles, much indirect evidence suggests that these microbes may play an important role in the coral holobiont, with respect to coral nutrition, health, and disease (14, 18, 30).It is now known that most microbes are uncultivable by present laboratory methods (1, 28, 10). To understand more about coral-associated microbial communities, to identify the diversity of microbes associated with particular corals, and to assess whether these microbes are indeed species specific or represent only opportunistic interactions with the coral animal, some relatively comprehensive studies have been carried out in recent years based on culture-independent molecular techniques, e.g., construction of 16S rRNA gene clone libraries or denaturing gradient gel electrophoresis (3, 6, 9, 11, 13, 16, 17, 19, 20, 21, 23, 30, 31, 33). Consequently, coral-associated microbes are now known to be not only highly diverse and dynamic but also substantially coral specific.Recently, the specificity of association between coral and bacterial species has been a topic of much discussion. Earlier reports suggested that similar microbial communities were specifically associated with identical coral species, regardless of whether they were isolated from distinct geographic regions or at different times (3, 9, 20, 21); however, environmental factors have also recently been found to significantly influence the specificity of bacteria-coral associations (2, 17). Such inconsistency might reasonably be expected in light of the complexity of interaction in the coral holobiont, which includes coral, algae, fungi, bacteria, archaea, and other biotic and environmental factors (30). Nonetheless, more-detailed studies are needed for a better comprehension of species-specific bacterial associations.In this study, we selected Stylophora pistillata, a widely distributed coral in western Pacific reefs (26), to study the diversity and composition of the coral-associated bacteria and the effects of spatial and temporal differences on such population structures. We also examined the species specificity of such coral-bacteria associations by comparing our data with another 44 coral-associated bacterial data sets. This biodiversity analysis shows the presence of a large variation in the composition of S. pistillata-associated bacterial communities, suggesting that specificity between S. pistillata and associated bacteria is significantly influenced by geographic and seasonal factors. Furthermore, a comparison with 10 previous studies of coral-associated microbes showed that spatial and temporal factors play a role in affecting the population structure of coral-associated bacteria, though distinct species-specific bacterial profiles are detectable in some corals of the Caribbean Sea.     

山东五莲山植物群落结构及物种多样性

五莲山自然保护区地处鲁东南沿海地区,为全面了解其群落结构组成及物种多样性,作者进行了野外调查,共获得11个标准样方,面积6 600 m²。样方内记录到高等植物52科141种。该保护区地带性植被为常绿—落叶针阔叶天然次生混交林、落叶阔叶林,主要森林植被为赤松—板栗群落(Pinus densiflora-Castanea mollissima community)、麻栎—赤松群落(Quercus acutissima-Pinus densiflora community)、赤松—杜鹃群落（P. densiflora-Rhododendron simsii community）、麻栎—杜鹃群落(Q. acutissima-Rhododendron simsii community)。样方数据显示该区域木本植物种类不是很丰富,但植物群落结构复杂,具有明显的生境异质性,其多样性指数乔木层＜木本层＜灌木层。作者认为影响该保护区核心区多样性的最显著特征应该为海拔和坡度,而人为干扰会严重影响外围保护区植被类型及其物种多样性。整体上看,本区域正处于群落演替早期,种间竞争尚不充分,物种多样性偏低。     

Saltwater Intrusion Modifies Microbial Community Structure and Decreases Denitrification in Tidal Freshwater Marshes

Ecosystems - Environmental changes can alter the interactions between biotic and abiotic ecosystem components in tidal wetlands and therefore impact important ecosystem functions. The objective of...     

Diversity and Community Structure of Primary Wood-Inhabiting Bacteria in Boreal Forest

DNA-based pyrosequencing analysis of the V1- V3 16S rRNA gene region was used to identify bacteria community and shift during early stages of wood colonization in boreal forest soils. The dataset comprised 142,447 sequences and was affiliated to 11 bacteria phyla, 25 classes and 233 genera. The dominant groups across all samples were Proteobacteria, followed by Bacteroidetes, Acidobacteria, Actinobacteria, Amatimonadetes, Planctomycetes and TM7 group. The community structure of the primary wood-inhabiting bacteria differed between types of forest soils and the composition of bacteria remained stable over prolonged incubation time. The results suggest that variations in soil bacterial community composition have an influence on the wood-inhabiting bacterial structure.     

Nitrite Removal Performance and Community Structure of Nitrite-Oxidizing and Heterotrophic Bacteria Suffered with Organic Matter

Altlhough ammonia oxidation and ammonia-oxidizing bacteria (AOB) have been extensively studied, nitrite oxidation and nitrite-oxidizing bacteria (NOB) are still not well understood. In this article, the effect of organic matter on NOB and heterotrophic bacteria was investigated with functional performance analysis and bacterial community shift analysis. The results showed that at low concentrations of initial sodium acetate [initial sodium acetate (ISA) = 0.5 or 1 g/L], the nitrite removal rate was higher than that obtained under autotrophic conditions and the bacteria had a single growth phase, whereas at high ISA concentrations (5 or 10 g/L), continuous aerobic nitrification and denitrification occurred in addition to higher nitrite removal rates, and the bacteria had double growth phases. The community structure of total bacteria strikingly varied with the different concentrations of ISA; the dominant populations shifted from autotrophic and oligotrophic bacteria (NOB, and some strains of Bacteroidetes, Alphaproteobacteria, Actinobacteria, and green nonsulfur bacteria) to heterotrophic and denitrifying bacteria (strains of Gammaproteobacteria, especially Pseudomonas stutzeri and P. nitroreducens). The reasons that nitrite removal rate increased with supplement of organic matters were discussed.     

On the Species Structure of a Competitive Marine Community

Some examples of marine animal and plant communities with a structure determined by competitive inter-species relationships are discussed. It has been shown that the ranked species structure of these communities obeys a geometric progression, whose coefficient does not differ significantly from the constant exp(–1) = 0.368. A relationship between a certain parameter of this progression and the species diversity of a community has been found.     

Bacterial Density and Community Structure Associated with Aggregate Size Fractions of Soil-Feeding Termite Mounds

The building and foraging activities of termites are known to modify soil characteristics such as the heterogeneity. In tropical savannas the impact of the activity of soil-feeding termites (Cubitermes niokoloensis) has been shown to affect the properties of the soil at the aggregate level by creating new soil microenvironments (aggregate size fractions) [13]. These changes were investigated in greater depth by looking at the microbial density (AODC) and the genetic structure (automated rRNA intergenic spacer analysis: ARISA) of the communities in the different aggregate size fractions (i.e., coarse sand, fine sand, coarse silt, fine silt, and dispersible clays) separated from compartments (internal and external wall) of three Cubitermes niokoloensis mounds. The bacterial density of the mounds was significantly higher (1.5 to 3 times) than that of the surrounding soil. Within the aggregate size fractions, the termite building activity resulted in a significant increase in bacterial density within the coarser fractions (>20 m). Multivariate analysis of the ARISA profiles revealed that the bacterial genetic structures of unfractionated soil and soil aggregate size fractions of the three mounds was noticeably different from the savanna soil used as a reference. Moreover, the microbial community associated with the different microenvironments in the three termite mounds revealed three distinct clusters formed by the aggregate size fractions of each mound. Except for the 2–20 m fraction, these results suggest that the mound microbial genetic structure is more dependent upon microbial pool affiliation (the termite mound) than on the soil location (aggregate size fraction). The causes of the specificity of the microbial community structure of termite mound aggregate size fractions are discussed.This revised version was published online in November 2004 with corrections to Volume 48.