Abstract
A polyphasic approach that included PCR-dependent and PCR-independent molecular techniques was applied to analyze the prokaryotic community in surface waters of shallow Antarctic lakes. The ...in situ abundance of different bacterial groups was determined by the fluorescence in situ hybridization, whereas bacterial diversity was investigated by 16S rRNA gene sequencing of bacterial clones and isolates. The different approaches allowed the identification of the significant microbial components of the lake bacterioplanktonic communities, indicating a predominance of Flavobacterium, Pseudomonas, and Polaromonas (up to about 56% of total sequences). These genera also appear to be important in freshwater systems elsewhere in the world. Interestingly, closest blast matches to our sequences were predominantly from polar lakes and ponds, in addition to streams and glaciers, suggesting a bipolar distribution of freshwater lake bacterioplankton. Bacteria that are more traditionally associated with the marine environment were also detected, thus indicating an external input by atmospheric deposition and/or seabird excreta. Finally, a slightly different microbial community occurred in the lake at Inexpressible Island that was characterized by low N : P ratio and very high conductivity value, reinforcing the idea that physicochemical and trophic status may affect the structure and composition of the bacterioplankton assemblages in Antarctic lakes.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Coastal areas of the West Antarctic Peninsula (WAP) constitute a rich and biodiverse marine zone. Despite these ecosystems being supported by the microorganism’s activity, the structure of microbial ...communities is insufficiently studied. As WAP is the area most affected by global warming worldwide, the increased glacier melting caused by the global warming and the consequent increase of the water runoff could be deeply affecting these microbial communities. To advance knowledge about the structure of microbial communities and its response to the environmental factors, a full-year study of marine bacterioplankton was conducted at Potter Cove, Antarctica. Multivariate analysis based on denaturing gradient gel electrophoresis (DGGE) and environmental data revealed a seasonal pattern in the structure of the bacterioplankton community, with spring–summer clustering separately from autumn–winter samples. Salinity, temperature and particulated matter were the main environmental driving forces. Based on the seasonal patterns, five bacterial clone libraries were performed from three sampling sites (E1, inner cove; E2, outer cove; and E3, mouth of a creek). Phylogenetic analysis of libraries generated 301 operational taxonomic units (OTUs), revealing the enormous richness and high diversity of these communities. Proteobacteria (68%), Bacteroidetes (20%) and Actinobacteria (8%) were the most represented phyla. During summer, bacterial community from E1 resembled that observed in E3, whereas during winter it resembled the E2 community. Results evidenced the influence of glacial meltwater input and showed the high variability of the bacterioplankton from inner cove. This study contributes to the better understanding of the structure of the Potter Cove marine ecosystems and could be reflecting the behavior of other similar ecosystems from WAP.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OBVAL, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Wuyi Hong Qu (black-skin-red-koji) glutinous rice wine, as one of the most typical representatives of Hong Qu glutinous rice wine in Fujian province of China, is brewed under non-sterile and ...uncontrolled fermentation condition based on empirical knowledge, causing uncontrollability of fermentation process and instability of the final quality. The objective of this study was to investigate the bacterial dynamics during the traditional fermentation of Wuyi Hong Qu glutinous rice wine using PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and 16S ribosomal RNA (rRNA) gene clone libraries analysis.
The DGGE profile indicated that the dominant bacterial species in the traditional wine fermentation starters were Pediococcus pentosaceus, Pediococcus acidilactici and Bacillus sp. (including Bacillus aryabhattai or Bacillus megaterium and Bacillus amyloliquefaciens). Bacterial dynamic obtained from the PCR-DGGE revealed the presence of Bacillus sp. and LAB (including Lactobacillus plantarum group, Lactobacillus brevis, P. acidilactici and P. pentosaceus) during the traditional fermentation process, but they varied in different brewing phases. The relative proportions of some bacterial species (such as Bacillus sp., P. acidilactici, L. brevis and P. pentosaceus) detected at early fermentation stage decreased as the fermentation progressed. While L. plantarum group was consistently detected with high light band intensity throughout the fermentation process. 16S rRNA gene clone libraries revealed that the two different molecular biological methods gave similar results, but clone library analysis was more representative of the bacterial community to some extent. For example, Leuconostoc mesenteroides was detected by 16S rRNA gene clone library but not discovered by bacterial DGGE profile throughout the whole fermentation process. Therefore, the combined approach of nested PCR-DGGE and 16S rRNA gene clone libraries would give a more comprehensive profile of the bacterial dynamics than either alone. Finally, species-specific multiplex PCR was also performed to confirm the L. plantarum group. Result showed that only L. plantarum can be detected from the total bacterial DNA extracted from samples of different fermentation phases.
This is the first report to reveal the dynamics of bacterial species involved in Wuyi Hong Qu glutinous rice wine brewing process using culture-independent methods. It might be useful to control wine production systems and improve wine quality.
•Hong Qu glutinous rice wine is brewed with traditional fermentation starters.•We examine the bacterial dynamics by two culture-independent approaches.•LABs were the predominant bacterial species during traditional fermentation.•The potential functions of microorganisms in starters were discussed.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Spoilage bacteria in milk are controlled by treatments such as thermization, microfiltration and addition of carbon dioxide. However, little information is known about the changes in microbial ...communities during subsequent cold storage of treated milk. Culture-dependent methods and a direct molecular approach combining 16S rRNA gene clone libraries and quantitative PCR (Q-PCR) were applied to obtain a better overview of the structure and the dynamics of milk microbiota. Raw milk samples were treated by the addition of carbon dioxide (CO
2), thermization (TH) or microfiltration (MF) and stored at 4
°C or 8
°C up to 7
d. Untreated milk (UT) was used as a control. Psychrotrophic and staphylococci bacteria were enumerated in the milk samples by culture methods. For the molecular approach, DNA was extracted from milk samples and 16S rRNA gene was amplified by PCR with universal primers prior to cloning. The Q-PCR method was used to evaluate the dynamics of dominant bacterial species revealed by clone library analysis of 16S rRNA gene. Comparison of the 16S rRNA gene sequence indicated that the two most abundant operational taxonomic units (OTU), determined at 97% identity, belonged to the class
Gammaproteobacteria (40.3% of the 1415 sequences) and
Bacilli (40%). Dominant bacterial species in UT, CO
2 and TH milk samples at day 3 were affiliated with
Staphylococcus,
Streptococcus,
Clostridia,
Aerococcus,
Facklamia,
Corynebacterium,
Acinetobacter and
Trichococcus. Dominant bacterial species detected in MF milk were
Stenotrophomonas,
Pseudomonas and
Delftia, while
Pseudomonas species dominated the bacterial population of UT, CO
2 and MF milk samples at day 7.
Staphylococcus and
Delftia were the dominant bacterial species in thermized milk. Q-PCR results showed that populations of
S. aureus, A. viridans, A. calcoaceticus, C. variabile and
S. uberis were stable during 7
d of storage at 4
°C. Populations of
P. fluorescens, S. uberis and total bacteria increased in UT and CO
2 milk samples during 7
d of storage at 8
°C and were noticeable from day 3. This study shows new microbial species which can develop during cold storage after milk treatment and contributes to identifying causes of reduced shelf life and deterioration of technological properties of milk during storage.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
During the Arctic summer, bacteria are active above the permafrost in an environment with sharp temperature and oxygen gradients. The present study addressed the diversity and abundance of bacteria ...in soil layers near the surface and above the permafrost of the rim and center of a low-centered polygon in the Lena Delta, Siberia. 16S rRNA gene clone libraries revealed the presence of all major soil bacterial groups and of the candidate divisions OD1, OP5, and OP11, and indicated a small-scale heterogeneity of these polygonal tundra soils. The diversity at the top of the elevated polygon rim was significantly different from that of the bottom and from both water-saturated sites of the polygon's center. The overall species-level diversity was very high (Shannon index of 5.3) but varied within the sites and decreased towards the permafrost table, coinciding with decreasing dissolved organic carbon (DOC) and phosphate concentrations. According to the number of operational taxonomical units (OTUs) and cells visualized by fluorescence in-situ hybridization, Bacteroidetes and Actinobacteria were the dominant members of the bacterial community in all sites. Bacteroidetes contributed almost 50% to all Bacteria cells while sequences affiliated with Bacteroidetes/Chlorobi represented on average 23% of all OTUs. Our results provide evidence of the extremely diverse bacterial communities present in permafrost soils and of the influence of nutrient concentrations, oxygen, and DOC on diversity.
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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
Inland blue holes of the Bahamas are anchialine ecosystems with distinct fresh and salt water layers, and anoxic or microoxic conditions at depth. Scientific cave diving and geomicrobiology ...exploration of blue holes are providing a first glimpse of the geochemistry and microbial life in these vertically stratified karst features. We hypothesized that two geographically adjacent, sunlit blue holes on Abaco Island would have comparable biogeochemistry and microbial life. Water samples were analyzed using in situ multiparameter dataloggers and field and laboratory tests, and diver-retrieved microbial samples were analyzed using nucleic acid analysis. Microbial 16S rRNA genes were dominated by members of the anoxygenic phototroph clade Chlorobi, with smaller numbers of Deltaproteobacteria, in both blue holes. However, spatial distributions of microbial biomass and species present within these major clades were significantly different. We also found that differences in the intensity of solar insolation, terrestrial and marine inputs, water residence time, depth to the halo/chemocline, and cave passage geometry strongly influence geochemical changes with depth. The biogeochemical diversity of inland blue holes in the Bahamas make them valuable as natural laboratories, repositories of microbial diversity, and analogs for stratified and sulfidic oceans present early in Earth’s history.
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DOBA, EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, IZUM, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UILJ, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Copahue is an acidic geothermal volcanic region in the northwest corner of Neuquén Province, Argentina. In the area, there are various ponds, pools and hot springs with different temperatures, pH ...values and levels of anthropogenic influence. In this study, the prokaryotic biodiversity of five representative ponds was studied by using two complementary molecular ecology techniques: phylogenetic analysis of 16S rRNA bacterial and archaeal genes and FISH (or CARD-FISH) for quantitative estimation of biodiversity. The results, supported by multivariate statistical analysis, showed that the biodiversity in Copahue ponds seemed to be determined by temperature. High temperature ponds were dominated by archaea, mainly apparently novel representatives from the orders Sulfolobales and Thermoplasmatales that had no close cultivated relatives. By contrast, moderate temperature ponds were colonised by well-characterised sulphur-oxidising bacteria related to acidic environments, such as other geothermal sites or acid mine drainage, and archaea were absent. By combining the biodiversity results from this study and the reported physicochemical features of Copahue, a preliminary model of the possible biogeochemical interaction was outlined for moderate and high temperature ponds.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
Recent studies suggest that magnetic susceptibility (MS) measurements can play an important role in identifying zones where microbial-mediated iron mineral transformations are occurring. Here we ...investigated the microbial community variations within zones of elevated MS in a petroleum hydrocarbon-contaminated aquifer near Bemidji, Minnesota, USA. Our main objective was to 1) identify the key microbial populations that may play a role in hydrocarbon degradation, 2) analyze which microbial populations could be connected to the elevated MS and 3) explore the use of non-destructive geophysical techniques as a tool to guide microbial sampling. Clone libraries based on the 16S rRNA gene revealed the presence of iron-reducing β-Proteobacteria in the vadose zone, whereas the free petroleum phase on the water table was characterized by a methanogenic consortium, in which the syntrophic δ-proteobacterium Smithella and the hydrogenotrophic Methanoregula predominated. Nonmetric multidimensional scaling (NMDS) found a close relationship between elevated MS values and the methanogenic hydrocarbon-degrading consortium. Our results suggest that magnetic susceptibility measurements can guide microbiologists to zones of active microbial biodegradation in aged petroleum spills.
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BFBNIB, DOBA, GIS, IJS, IZUM, KILJ, KISLJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Benthic foraminifera are globally distributed protozoa in the world's oceans, which have been used as ecological indicators in both current and palaeo oceanography. The ecological properties and ...distribution of these organisms in various regions of the Gulf of Mexico (GOM) have been evaluated using microscopy; however molecular approaches for these purposes have been limited, especially in deeper regions. The BP Deepwater Horizon oil well failure in the northern Gulf of Mexico highlighted the need to better understand the distribution and abundance of these organisms relative to environmental factors and ecosystem perturbations such as the oil spill. Sediment samples were collected using a Shipek grab along transects on the northwest Florida GOM shelf (18–270m depth). Clone libraries were developed from PCR amplified 18S rDNA genes for sequence analysis. Analysis of random clones from libraries were used as a proxy for community structure (presence and relative abundance) to document the spatial and temporal dynamics of benthic foraminifera on the Northwest Florida Shelf in the NE GOM shelf. Additional continental slope samples (200–1600m depth) were obtained by a multicorer and treated in similar fashion. Mean species diversity in this study (H=2.49–3.36), agreed with pre-DWH event estimates, however the dominant agglutinated species in the deep-water samples did not match previous studies. Additionally, the dominant calcareous taxa from this study such as Allogromida sp. and Psammophaga sp., were inconsistent with previous reports. The dominant taxa in both coastal and deep-water sites include Glabratellina sp., Trochammina hadai, and Trochammina sp., and Textularia sagittula and Bathysiphon argenteus as well as members of genera Astrammina, Bolivina, Cibicides and Cibicidoides.
•Species diversity (Shannon-Wiener) ranged from 2.49 to 3.36.•Diversity values showed no correlation to increased PAHs•Dominant taxa in clone libraries include Glabratellina sp., Trochammina hadai, T. sp., and Textularia sagittula.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Background and aims Soil freeze-thaw cycle (FTC) regimes are altered by climate change and known to influence nutrient cycling and plant growth. Here, we explore mechanistic explanations for the ...changing plant performance of the grass Holcus lanatus and the dwarf shrub Calluna vulgaris. Methods 144 plant-soil mesocosms were subjected to different FTC-regimes in a climate chamber. Root injury, fungal activity and fungal composition (ITS-sequencing) were quantified. Results The applied FTC-scenarios increased root injury by 23% on average while no strong differences between scenarios was found. Root damage was greater in C. vulgaris than in H. lanatus. Fungal activity increased due to the FTC-manipulation and was higher in the C. vulgaris samples, although activity was generally low. No significant shift in the fungal community composition was found immediately after the applied FTCs. A saprobic (Aureobasidium pullulans) and a potentially mycorrhizal fungus (Sebacinales) showed opposing responses to the FTC-manipulation in the different host plants, while a potential phytopathogen (Callophora) decreased in frequency. Conclusions Increased fungal activity within these samples is suggested to be related to an increased dominance of saprobic taxa, but not to a shift in qualitative community composition. Single pathogenic species entering the plants through the observed root injuries subsequent to FTC treatments however, may alter plant performance. While these results suggest the importance of root injury for the response of vegetation to FTCs, fungal activity and pathogenic infection need to be further studied under field conditions over longer time periods.
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BFBNIB, DOBA, EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, IZUM, KILJ, KISLJ, MFDPS, NLZOH, NMLJ, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UILJ, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
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