Cyanobacteria are generally thought to be responsible for primary production and nitrogen fixation in the microbial communities that dominate Antarctic ecosystems. Recent studies of bacterial ...communities in terrestrial Antarctica, however, have shown that Cyanobacteria are sometimes only scarcely present, suggesting that other bacteria presumably take over their role as primary producers and diazotrophs. The diversity of key genes in these processes was studied in surface samples from the Sør Rondane Mountains, Dronning Maud Land, using clone libraries of the large subunit of ribulose-1,5-biphosphate carboxylase/oxygenase (RuBisCO) genes (cbbL, cbbM) and dinitrogenase-reductase (nifH) genes. We recovered a large diversity of non-cyanobacterial cbbL type IC in addition to cyanobacterial type IB, suggesting that non-cyanobacterial autotrophs may contribute to primary production. The nifH diversity recovered was predominantly related to Cyanobacteria, particularly members of the Nostocales. We also investigated the occurrence of proteorhodopsin and anoxygenic phototrophy as mechanisms for non-Cyanobacteria to exploit solar energy. While proteorhodopsin genes were not detected, a large diversity of genes coding for the light and medium subunits of the type 2 phototrophic reaction center (pufLM) was observed, suggesting for the first time, that the aerobic photoheterotrophic lifestyle may be important in oligotrophic high-altitude ice-free terrestrial Antarctic habitats.
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BFBNIB, EMUNI, FZAB, GEOZS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NMLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UL, UM, UPUK, VKSCE, ZAGLJ
Biological desert crusts are relatively common in the arid deserts of the Sultanate of Oman; however, little is known about their microbial community composition and role in soil fertilization. We ...compared three crusts from geographically different locations for their soil texture, bacterial community structure, pigment composition and nitrogenase activity. The crusts were growing on alkaline (pH 7.6-8.7) loamy sand and silty loam soils. Microscopically, Microcoleus vaginatus was the most abundant cyanobacterium, but Nostoc and Scytonema types dominated in cultures. The 16S rRNA gene sequences showed close similarities in the crusts' bacterial composition, with 77-81% of the total clones belonging to cyanobacteria and the rest distributed among Alpha- and Deltaproteobacteria, Bacteriodetes, Gemmatimonas and Planctomycetes. Thirty-seven percent of the cyanobacterial clones were affiliated with heterocystous types such as Nostoc, Scytonema, Brasilonema and Petalonema. Chlorophyll a concentrations suggest a similar abundance of phototrophs in all crusts. High levels of the UVA sunscreen scytonemin were detected in the exposed crusts. The three crusts exhibited comparable acetylene reduction rates in the light and in the dark, with a maximum rate of 58.5±2.6 μmol C₂H₂ reduced m⁻² h⁻¹. We conclude that the crusts, regardless of their geographical location, were rich in heterocystous cyanobacteria that can fix nitrogen and could possibly improve soil stability and productivity.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Flooded rice paddy soils represent a typical anaerobic freshwater habitat of microorganisms. The abundance and community structure of sulfate reducing prokaryotes (SRP) were investigated in order to ...understand their response to different fertilization practices in rice paddy, including control without fertilizers (CT) and arrangements of different chemical fertilizers of nitrogen (N), phosphorus (P) and potassium (K): N, NP, NK and NPK. The abundance of total bacteria and sulfate reducing prokaryotes of the rice paddy in summer and in winter were quantified by real-time PCR assays based on the 16S rRNA gene and the dissimilatory (bi)sulfite reductase gene (
dsrAB) β-subunit. No significant differences in the bacterial and SRP abundance were observed among different fertilization treatments in both winter and summer. The mean copy numbers of bacteria was 7.26
×
10
9
copies g
−1 dry soil in winter and 1.27
×
10
10
copies g
−1 dry soil in summer. The average
dsrAB gene copy numbers of the SRP was 5.08
×
10
8
copies g
−1 dry soil in winter and 5.92
×
10
8
copies g
−1 dry soil in summer. The
dsrAB gene clone libraries of the five fertilization treatments were constructed and their RFLP analysis yielded 22–25 restriction patterns, suggesting a high degree of
dsrAB sequence diversity in different fertilization treatments. There was no significant change in the soil SRP community structure among the different fertilization regimes. More than half of the sequences were affiliated with novel branching clusters which were uncultured SRP.
Clostridia and
Deltaproteobacteria were also found with a high proportion in the clone libraries, while
Desulfovibrionaceae was absent. High proportion of novel uncultured SRP implies that they may play important roles in paddy soils and deserve further studies.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
The phylogenetic diversity and seasonal dynamics of free-living and particle-associated bacterial communities were investigated in the epilimnion of 4 lakes of the Mecklenburg Lake District, ...northeastern Germany. All lakes differed in their limnological features, ranging from oligotrophic to eutrophic and dystrophic. Bacterial community structure and seasonal dynamics were analyzed by denaturing gradient gel electrophoresis (DGGE) and clone libraries of 16S rRNA gene fragments. Communities of free-living and particle-associated bacteria greatly differed among the lakes. In addition, significant differences occurred between both bacterial fractions within each lake. Seasonal changes were more pronounced in free-living than in particle-associated bacterial communities. Non-metric multidimensional scaling (NMDS) analyses revealed several strong correlations between bacterial communities (both free-living and particle-associated) and environmental variables such as pH, dissolved organic carbon (DOC), phytoplankton biomasses, and primary production. Phylogenetically, all cloned and sequenced 16S rRNA gene fragments belonged to already known freshwater clusters. Clone libraries of free-living bacteria were dominated by sequences of Actinobacteria, Bacteroidetes, and Betaproteobacteria, whereas those of particle-associated bacteria predominantly consisted of Cyanobacteria and Bacteroidetes sequences. Other freshwater phyla such as Alpha- and Gammaproteobacteria, Verrucomicrobia, Planctomycetes, and members of Candidate Division OP10 were found in low proportions. These differences may indicate an adaptation of distinct bacterioplankton communities to the respective environmental conditions of each lake.
Abstract
Acropora white syndrome (AWS) is characterized by rapid tissue loss revealing the white underlying skeleton and affects corals worldwide; however, reports of causal agents are conflicting. ...Samples were collected from healthy and diseased corals and seawater around American Samoa and bacteria associated with AWS characterized using both culture-dependent and culture-independent methods, from coral mucus and tissue slurries, respectively. Bacterial 16S rRNA gene clone libraries derived from coral tissue were dominated by the Gammaproteobacteria, and Jaccard's distances calculated between the clone libraries showed that those from diseased corals were more similar to each other than to those from healthy corals. 16S rRNA genes from 78 culturable coral mucus isolates also revealed a distinct partitioning of bacterial genera into healthy and diseased corals. Isolates identified as Vibrionaceae were further characterized by multilocus sequence typing, revealing that whilst several Vibrio spp. were found to be associated with AWS lesions, a recently described species, Vibrio owensii, was prevalent amongst cultured Vibrio isolates. Unaffected tissues from corals with AWS had a different microbiota than normal Acropora as found by others. Determining whether a microbial shift occurs prior to disease outbreaks will be a useful avenue of pursuit and could be helpful in detecting prodromal signs of coral disease prior to manifestation of lesions.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Protistan community structure was examined from 6 depths (1.5, 20, 42, 150, 500, 880
m) at a coastal ocean site in the San Pedro Channel, California. A total of 856 partial length 18S rDNA protistan ...sequences from the six clone libraries were analyzed to characterize diversity present at each depth. The sequences were grouped into a total of 259 Operational Taxonomic Units (OTUs) that were inferred using an automated OTU calling program that formed OTUs with approximately species-level distinction (95% sequence similarity). Most OTUs (194 out of 259) were observed at only one specific depth, and only two were present in clone libraries from all depths. OTUs were obtained from 21 major protistan taxonomic groups determined by their closest BLAST matches to identified protists in the NCBI database. Approximately 74% of the detected OTUs belonged to the Chromalveolates, with Group II alveolates making up the largest single group. Protistan assemblages at euphotic depths (1.5, 20 and 42
m) were characterized by the presence of clades that contained phototrophic species (stramenopiles, chlorophytes and haptophytes) as well as consumers (especially ciliates). Assemblages in the lower water column (150, 500 and 800
m) were distinct from communities at shallow depths because of strong contributions from taxa belonging to euglenozoans, acantharians, polycystines and Taxopodida (
Sticholonche spp. and close relatives). Species richness (Chao I estimate) and diversity (Shannon index) were highest within the euphotic zone and at 150
m, and lowest for protistan assemblages located in the oxygen minimum zone (500 and 880
m). Multivariate analyses (Bray–Curtis coefficient) confirmed that protistan assemblage composition differed significantly when samples were grouped into shallow (≤150
m) and deep water assemblages (≥150
m).
► Protistan community structure and diversity varies distinct with depth. ► Protistan species diversity indicated as lower within oxygen minimum zone. ► Novel alveolates important within protistan assemblages throughout water column. ► Rhizaria highly abundant in clone libraries from aphotic depths.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Pseudo-nitzschia-specific PCR primers (PnAll F/R) were designed to amplify a polymorphic region of the internal transcribed spacer 1 (ITS1) from at least 11 Pseudo-nitzschia species. The primers were ...used to generate environmental clone libraries from Puget Sound, Washington, and Vancouver Island, British Columbia, to confirm that the primers were specific for Pseudo-nitzschia and to determine the extent of ITS1 sequence diversity within individual species. All environmental ITS1 sequences generated with PnAll primers displayed the greatest similarity to known Pseudo-nitzschia ITS1 sequences. The length of cloned ITS1 fragments differed among species but was conserved within a species. Intraspecific genotypes exhibited <3% sequence divergence for seven of the 10 species detected in clone libraries. Several ITS1 genotypes unique to the Pacific Northwest were identified in environmental samples, and other genotypes were more broadly distributed. The Pseudo-nitzschia primers were also used to develop an automated ribosomal intergenic spacer analysis (ARISA) to rapidly identify Pseudo-nitzschia species in environmental samples based on species-specific variation in the length of the targeted ITS1 region. The ARISA peaks were then associated with the environmental clone sequences for Pseudo-nitzschia species. Surveying the genetic composition of communities at both the inter- and intraspecific levels will enhance our understanding of Pseudo-nitzschia bloom dynamics.
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BFBNIB, DOBA, FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, UILJ, UKNU, UL, UM, UPUK
The objective of this work was to develop protocols to selectively extract prokaryotic DNA from soils, representative of the whole community, amenable to high-throughput whole genome shotgun ...sequencing. Prokaryotic cells were extracted from soils by blending, followed by gradient centrifugation. Detergent (sodium deoxycholate) was required for complete dispersion of soil aggregates and detachment of prokaryotic cells from a broad range of soil types. Repeated extractions of a given soil sample were critical to maximize cell yield. Furthermore, cells obtained through repeated extractions captured unique prokaryotic assemblages that would otherwise have been missed in single-pass extractions. DNA was isolated from extracted cells using one of the following treatments: i) lysozyme–SDS–proteinase K (enzymatic) digestion; ii) potassium ethyl xanthogenate digestion; or iii) enzymatic digestion of cells embedded in agarose plugs. In addition, these methods were compared to a commercial bead-beating extraction kit (MoBio UltraClean). Of the indirect DNA extraction methods, plug digestion generated the largest yields (up to 70% of yields obtained by direct DNA extraction) of high-molecular weight DNA (>400
kb). Thus, plug digestion is amenable to large-insert metagenomic library construction and analysis. Comparisons of banding patterns generated by RAPD-PCR and DGGE indicated that sequence composition and inferred community composition of a given extract varied greatly with DNA isolation method. While overall diversity did not change significantly with the cell lysis method, analysis of 16S rRNA gene clone libraries revealed that each extraction procedure produced unique distributions of prokaryotic phyla within the sample population.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
The overwintering deployment of an icebreaker during the Canadian Flaw Lead study provided an opportunity to evaluate how protist communities (phytoplankton and other single-celled eukaryotes) ...respond to changing spring irradiance conditions in flaw lead polynyas, where open water persists between the central pack ice and land fast ice. We combined microscopic analysis of the protist communities (all cell sizes) with clone libraries of 18S rRNA genes and 18S rRNA (from RNA converted to cDNA) of size-fractionated seawater (0.2–3.0 μm) from 10 to 12 m depth in the surface mixed layer. The rRNA gene analysis provided information on the presence of organisms, while the rRNA analysis provided information on the most active members of the community. There was little overlap between the two types of clone libraries, and there were large community shifts over time. Heterotrophic dinoflagellates and ciliates were the most common sequences recovered. The relative proportion of photosynthetic protist sequences increased in March and April, and there was greater representation of Bacillariophyta, Prasinophyta, Haptophyta, and Cryptophyta in the rRNA compared to rRNA gene libraries. Microscopy indicated that large-celled diatoms dominated the community in May, when chlorophyll concentrations were greatest. However, the RNA sequencing showed that heterotrophic and putative parasitic protists were proportionately more active, and the concomitant decrease in nutrients suggested that the spring phytoplankton bloom had begun to decline by this time. These observations provide evidence of substantial changes in protist community structure and function during the spring transition.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
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