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1.
Baati H Guermazi S Amdouni R Gharsallah N Sghir A Ammar E 《Extremophiles : life under extreme conditions》2008,12(4):505-518
16S rRNA gene clone libraries were separately constructed from three ponds with different salt concentrations, M2 (15%), TS38
(25%) and S5 (32%), located within a multipond solar saltern of Sfax. The 16S rRNA genes from 216 bacterial clones and 156
archaeal clones were sequenced and phylogenetically analyzed. 44 operational taxonomic units (OTUs) were generated for Bacteria and 67 for Archaea. Phylogenetic groups within the bacterial domain were restricted to Bacteroidetes and Proteobacteria, with the exception that one cyanobacterial OTU was found in the TS38 pond. 85.7, 26.6 and 25.0% of the bacterial OTUs from
M2, TS38 and S5 ponds, respectively, are novel. All archaeal 16S rRNA gene sequences were exclusively affiliated with Euryarchaeota. 75.0, 60.0 and 66.7% of the OTUs from, respectively, M2, TS38 and S5 ponds are novel. The result showed that the Tunisian
multipond solar saltern harbored novel prokaryotic diversity that has never been reported before for solar salterns. In addition,
diversity measurement indicated a decrease of bacterial diversity and an increase of archaeal diversity with rising salinity
gradient, which was in agreement with the previous observation for thalassohaline systems. Comparative analysis showed that
prokaryotic diversity of Tunisian saltern was higher than that of other salterns previously studied.
A. Sghir and E. Ammar have equally contributed to this work. 相似文献
2.
We investigated the bacterial diversity of microbial communities in water-filled, human-made and natural container habitats
of the mosquitoes Aedes aegypti and Aedes albopictus in suburban landscapes of New Orleans, Louisiana in 2003. We collected water samples from three classes of containers, including
tires (n = 12), cemetery urns (n = 23), and miscellaneous containers that included two tree holes (n = 19). Total genomic DNA was extracted from water samples, and 16S ribosomal DNA fragments (operational taxonomic units,
OTUs) were amplified by PCR and separated by denaturing gradient gel electrophoresis (DGGE). The bacterial communities in
containers represented diverse DGGE-DNA banding patterns that were not related to the class of container or to the local spatial
distribution of containers. Mean richness and evenness of OTUs were highest in water samples from tires. Bacterial phylotypes
were identified by comparative sequence analysis of 90 16S rDNA DGGE band amplicons. The majority of sequences were placed
in five major taxa: Alpha-, Beta- and Gammaproteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, and an unclassified group; Proteobacteria and Bacteroidetes were the predominant heterotrophic bacteria in containers. The bacterial communities in human-made containers consisted mainly
of undescribed species, and a phylogenetic analysis based on 16S rRNA sequences suggested that species composition was independent
of both container type and the spatial distribution of containers. Comparative PCR-based, cultivation-independent rRNA surveys
of microbial communities associated with mosquito habitats can provide significant insight into community organization and
dynamics of bacterial species.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
3.
Moez Bouali Eric Pelletier Sébastien Chaussonnerie Denis Le Paslier Amina Bakhrouf Abdelghani Sghir 《Applied microbiology and biotechnology》2013,97(9):4221-4231
Performance of biological wastewater treatment systems may be related to the composition and activity of microbial populations they contain. However, little information is known regarding microbial community inhabiting these ecosystems. The purpose of this study was to investigate archaeal and bacterial diversity, using cultivation-independent molecular techniques, in a constructed wetland receiving domestic wastewater. Two 16S rRNA gene libraries were constructed using total genomic DNA and amplified by PCR using primers specific for archaeal and bacterial domains. A high microbial diversity was detected. The Proteobacteria phylum is the most abundant and diversified phylogenetic group representing 31.3 % of the OTUs, followed by the Bacteroidetes (14.8 %), Planctomycetales (13.8 %), Actinobacteria (12 %), and Chloroflexi (8.2 %). Sequences affiliated with minor phylogenetic divisions such as the TM7, Nitrospira, OP10, and BRC1 are represented by <6 % of total OTUs. The Archaea domain was represented by the Thaumarchaeota phylum dominated by the Candidatus Nitrososphaera genus. 相似文献
4.
Cultivation based and culture independent molecular approaches were used to characterize the composition and structure of
bacterial community from a natural warm spring in the Western Ghats, a biodiversity ‘hotspot’. Dilution plating was done on
three types of media with varying nutrient levels. Relatively nutritionally poor medium supported growth of highest number
of bacteria (4.98 × 103 ml−1) compared to nutritionally rich media. On the basis of different morphological features on the plate, 62 aerobic and heterotrophic
bacterial strains were isolated and their 16S rRNA genes were sequenced and analyzed. On the basis of sequence similarity
these isolates were found to be distributed in 21 different genera belonging to Proteobacteria (58%) followed by Firmicutes (26%), Actinobacteria (13%) and Bacteroidetes (3%). Amplification of 16S rRNA gene of the community DNA using eubacterial primers, followed by cloning and sequencing revealed
that predominant members of the habitat belong to the phylum Cyanobacteria (60%) followed by Proteobacteria (19.5%), Bacteroidetes (6.67%), Actinobacteria (4.4%) and Firmicutes (2.2%) and small ribosomal subunit of a plastid (of Chlorophyta, 2.2%). 相似文献
5.
Molecular Diversity of the Rumen Microbiome of Norwegian Reindeer on Natural Summer Pasture 总被引:2,自引:0,他引:2
Sundset MA Edwards JE Cheng YF Senosiain RS Fraile MN Northwood KS Praesteng KE Glad T Mathiesen SD Wright AD 《Microbial ecology》2009,57(2):335-348
The molecular diversity of the rumen microbiome was investigated in five semi-domesticated adult female Norwegian reindeer
(Rangifer tarandus tarandus) grazing on natural summer pastures on the coast of northern Norway (71.00° N, 25.30° E). Mean population densities (numbers
per gram wet weight) of methanogenic archaea, rumen bacteria and ciliate protozoa, estimated using quantitative real-time
polymerase chain reaction (PCR), were 3.17 × 109, 5.17 × 1011 and 4.02 × 107, respectively. Molecular diversity of rumen methanogens was revealed using a 16S rRNA gene library (54 clones) constructed
using pooled PCR products from the whole rumen contents of the five individual reindeer. Based upon a similarity criterion
of <97%, a total of 19 distinct operational taxonomic units (OTUs) were identified, nine of which are potential new species.
The 16S rRNA sequences generated from the reindeer rumen exhibited a high degree of sequence similarity to methanogens affiliated
with the families Methanobacteriaceae (14 OTUs) and Methanosarcinaceae (one OTU). Four of the OTUs detected belonged to a
group of uncultivated archaea previously found in domestic ruminants and thought to be dominant in the rumen together with
Methanobrevibacter spp. Denaturing gradient gel electrophoresis profiling of the rumen bacterial 16S rRNA gene and the protozoal 18S rRNA gene
indicated a high degree of animal variation, although some bands were common to all individuals. Automated ribosomal intergenic
spacer analysis (ARISA) profiling of the ruminal Neocallimastigales population indicated that the reindeer are likely to contain more than one type of anaerobic fungus. The ARISA profile from
one animal was distinct from the other four. This is the first molecular investigation of the ruminal methanogenic archaea
in reindeer, revealing higher numbers than expected based on methane emission data available. Also, many of the reindeer archaeal
16S rRNA gene sequences were similar to those reported in domesticated ruminants in Australia, Canada, China, New Zealand
and Venezuela, supporting previous findings that there seems to be no host type or geographical effect on the methanogenic
archaea community structure in ruminants. 相似文献
6.
Several molecular techniques were employed to document the bacterial diversity associated with the marine sponge Gelliodes carnosa. Cultivation-dependent and cultivation-independent methods were used to obtain the 16S rRNA gene sequences of the bacteria.
Phylogenetic analysis based on the 16S rRNA gene sequences showed that the bacterial community structure was highly diverse
with representatives of the high G + C Gram-positive bacteria, cyanobacteria, low G + C Gram-positive bacteria, and proteobacteria
(α-, β-, and γ-), most of which were also found in other marine environments, including in association with other sponges. Overall,
300 bacterial isolates were cultivated, and a total of 62 operational taxonomic units (OTUs) were identified from these isolates
by restriction fragment length polymorphism (RFLP) analysis and DNA sequencing of the 16S rRNA genes. Approximately 1,000
16S rRNA gene clones were obtained by the cultivation-independent method. A total of 310 clones were randomly selected for
RFLP analysis, from which 33 OTUs were acquired by further DNA sequencing and chimera checking. A total of 12 cultured OTUs
(19.4% of the total cultured OTUs) and 13 uncultured OTUs (39.4% of the total uncultured OTUs) had low sequence identity (≤97%)
with their closest matches in GenBank and were probably new species. Our data provide strong evidence for the presence of
a diverse variety of unidentified bacteria in the marine sponge G. carnosa. A relatively high proportion of the isolates exhibited antimicrobial activity, and the deferred antagonism assay showed
that over half of the active isolates exhibited a much stronger bioactivity when grown on medium containing seawater. In addition
to demonstrating that the sponge-associated bacteria could be a rich source of new biologically active natural products, the
results may have ecological implications. This study expands our knowledge of the diversity of sponge-associated bacteria
and contributes to the growing database of the bacterial communities within sponges. 相似文献
7.
Diversity and quantity of ammonia-oxidizing Archaea and Bacteria in sediment of the Pearl River Estuary, China 总被引:2,自引:0,他引:2
Jin T Zhang T Ye L Lee OO Wong YH Qian PY 《Applied microbiology and biotechnology》2011,90(3):1137-1145
The diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the sediment of the
Pearl River Estuary were investigated by cloning and quantitative real-time polymerase chain reaction (qPCR). From one sediment
sample S16, 36 AOA OTUs (3% cutoff) were obtained from three clone libraries constructed using three primer sets for amoA gene. Among the 36 OTUs, six were shared by all three clone libraries, two appeared in two clone libraries, and the other
28 were only recovered in one of the libraries. For AOB, only seven OTUs (based on 16S rRNA gene) and eight OTUs (based on
amoA gene) were obtained, showing lower diversity than AOA. The qPCR results revealed that AOA amoA gene copy numbers ranged from 9.6 × 106 to 5.1 × 107 copies per gram of sediment and AOB amoA gene ranged from 9.5 × 104 to 6.2 × 105 copies per gram of sediment, indicating that the dominant ammonia-oxidizing microorganisms in the sediment of the Pearl River
Estuary were AOA. The terminal restriction fragment length polymorphism results showed that the relative abundance of AOB
species in the sediment samples of different salinity were significantly different, indicating that salinity might be a key
factor shaping the AOB community composition. 相似文献
8.
Bacterial diversity in five Icelandic geothermal waters: temperature and sinter growth rate effects 总被引:1,自引:0,他引:1
The microbial ecology associated with siliceous sinters was studied in five geochemically diverse Icelandic geothermal systems.
Bacterial 16S rRNA clone libraries were constructed from water-saturated precipitates from each site resulting in a total
of 342 bacterial clone sequences and 43 species level phylotypes. In near-neutral, saline (2.6–4.7% salinity) geothermal waters
where sinter growth varied between 10 and ~300 kg year−1 m−2, 16S rRNA gene analyses revealed very low (no OTUs could be detected) to medium (9 OTUs) microbial activity. The most dominant
phylotypes found in these waters belong to marine genera of the Proteobacteria. In contrast, in alkaline (pH = 9–10), meteoric geothermal waters with temperature = 66–96°C and <1–20 kg year−1m−2 sinter growth, extensive biofilms (a total of 34 OTUs) were observed within the waters and these were dominated by members
of the class Aquificae (mostly related to Thermocrinis), Deinococci (Thermus species) as well as Proteobacteria. The observed phylogenetic diversity (i.e., number and composition of detected OTUs) is argued to be related to the physico-chemical
regime prevalent in the studied geothermal waters; alkaliphilic thermophilic microbial communities with phylotypes related
to heterotrophic and autotrophic microorganisms developed in alkaline high temperature waters, whereas halophilic mesophilic
communities dominated coastal geothermal waters. 相似文献
9.
Olapade OA 《Microbial ecology》2012,63(1):96-102
The diel change in abundance and community diversity of the bacterioplankton assemblages within the Pacific Ocean at a fixed
location in Monterey Bay, California (USA) were examined with several culture-independent (i.e., nucleic acid staining, fluorescence
in situ hybridization {FISH}, and 16S ribosomal RNA gene libraries) approaches over a tidal cycle. FISH analyses revealed
the quantitative predominance of bacterial members belonging to the Cytophaga-Flavobacterium cluster as well as two Proteobacteria (α- and γ-) subclasses within the bacterioplankton assemblages, especially during high tide (HT) and outgoing tide (OT) than
the other tidal events. While the clone libraries showed that majority of the sequences were similar to the 16S rRNA gene
sequences of unknown bacteria (32% to 73%), however, the operational taxonomic units from members of the α-Proteobacteria, Bacteroidetes, Firmicutes, and Cyanobacteria were also well represented during the four tidal events examined. Comparatively, sequence diversity was highest in OT, lowest
in low tide, and very similar between HT and incoming tide. The results indicate that the dynamics of bacterial occurrence
and diversity appeared to be more pronounced during HT and OT, further indicative of the ecological importance of several
environmental variables including temperature, light intensity, and nutrient availability that are also concurrently fluctuating
during these tidal events in marine systems. 相似文献
10.
Addition of allochthonous fungi to a historically contaminated soil affects both remediation efficiency and bacterial diversity 总被引:1,自引:0,他引:1
Federici E Leonardi V Giubilei MA Quaratino D Spaccapelo R D'Annibale A Petruccioli M 《Applied microbiology and biotechnology》2007,77(1):203-211
Botryosphaeria rhodina DABAC P82 and Pleurotus pulmonarius CBS 664.97 were tested for their ability to grow and to degrade aromatic hydrocarbons in an aged contaminated soil. To evaluate
the impact of indigenous microflora on the overall process, incubations were performed on both fumigated and nonfumigated
soils. Fungal colonization by B. rhodina was unexpectedly lower in the fumigated than in the nonfumigated soil while the growth of P. pulmonarius showed an opposite response. Degradation performances and detoxification by both fungi in the nonfumigated soil were markedly
higher than those observed in the fumigated one. Heterotrophic bacterial counts in nonfumigated soil augmented with either
B. rhodina or P. pulmonarius were significantly higher than those of the corresponding incubation control (6.7 ± 0.3 × 108 and 8.35 ± 0.6 × 108, respectively, vs 9.2 ± 0.3 × 107). Bacterial communities of both incubation controls and fungal-augmented soil were compared by numerical analysis of denaturing
gradient gel electrophoresis profiles of polymerase chain reaction (PCR)-amplified 16S ribosomal RNA (rRNA) genes and cloning
and sequencing of PCR-amplified 16S rRNA genes. Besides increasing overall diversity, fungal augmentation led to considerable
qualitative differences with respect to the pristine soil. 相似文献
11.
Denaturing gradient gel electrophoresis (DGGE) analysis
of bacterial community composition in deep-sea sediments of the South China Sea 总被引:5,自引:0,他引:5
Xintian Lai Xiaofan Zeng Shu Fang Yali Huang Lixiang Cao Shining Zhou 《World journal of microbiology & biotechnology》2006,22(12):1337-1345
The South China Sea, which is one of the largest marginal seas in the world, is predicted to have suitable accumulation conditions and exporting prospects for natural gas hydrate. The aim of this study was to explore the bacterial community composition of deep-sea sediments from such an ecosystem. DNA was extracted by five different methods and used as templates for PCR amplification of the V3 regions of the 16S rRNA gene. Denaturing gradient gel electrophoresis (DGGE) was used to separate the amplified products and analyse the 16S rRNA gene diversity of sediment samples. The results of DGGE indicated that the bacterial community composition is influenced by DNA extraction methods. Sequencing dominant bands demonstrated that the major phylogenetic groups identified by DGGE belong to Proteobacteria, Bacteroidetes, gram-positive bacteria and Archaea. Integrating different DNA extraction procedures are needed to analyse the actual bacterial diversity from environment when the amplification of 16S rRNA gene and construction of representative clone library were adopted. 相似文献
12.
Trine Glad Vibeke Fam Kristiansen Kaare M. Nielsen Lorenzo Brusetti André-Denis G. Wright Monica A. Sundset 《Microbial ecology》2010,60(2):320-330
Dominant colonic bacteria in wild hooded (n = 9), harbour (n = 1) and grey (n = 1) seals were identified using 16S rRNA gene clone libraries (313 clones), revealing 52.7% Bacteroidetes, 41.5% Firmicutes, 4.5% Proteobacteria and 1.0% Fusobacteria. Thirty (77%) of the 39 phylotypes identified were novel, showing <97% sequence similarity to their nearest cultivated relatives.
Mean colonic bacterial cell density, determined by real-time PCR, was high (12.8 log10 cells/g wet wt) for the hooded seals, while the number of methanogenic Archea was low (4.0 log10 cells/g wet wt). The level of ampicillin (ampr) and tetracycline-resistant (tetr) isolates was investigated by cultivation. Aerobic ampr isolates were only detected in colon contents from four hooded seals, whereas aerobic tetr isolates were found in seven of the nine hooded seals. These data provide novel insight to the gut microbiota of Arctic and
sub-Arctic seals living in the wild. 相似文献
13.
The Pacific nodule province covers about 4.5 million km2 in the eastern tropical Pacific with abundance of polymetallic nodules. Microbes are believed to play large roles in the
metal cycling in many environments, but the microbial community in the Pacific nodule province has never been studied. Phylogenetic
studies based on 16S rRNA gene sequence analysis, together with bacterial cultivation were used to study the microbial populations
in the Pacific nodule province (A core) deep-sea sediment. Bacterial 16S rRNA gene sequence analysisdemonstrated that Proteobacteria division mainly of γ-Proteobacteria dominated the microbial community of the nodule province A core. Among the γ-Proteobacteria, Shewanella species which were known as Fe(□), Mn(□) reducing bacteria were found prevalent. Besides Proteobacteria, Green nonsulfur bacteria, the candidate subdivision OP3, Cytophaga-Flexibacter-Bacteroides bacteria and novel unidentified
strains were also detected. Archaeal 16S rDNA sequence analysis data and results from hybridization with crenarchaeotal marine
group I specific probe revealed that all archaea detected at the station belong to Crenarchaeota nonthermophilic marinegroup
I. Bacteria assigned to the gamma Proteobacteria wereisolated, none of them showed capability of manganese oxidation.
These authors contributed equally to this paper. 相似文献
14.
Phylogenetic and Physiological Diversity of Bacteria Isolated from Puruogangri Ice Core 总被引:2,自引:0,他引:2
The microbial abundance, the percentage of viable bacteria, and the diversity of bacterial isolates from different regions
of a 83.45-m ice core from the Puruogangri glacier on the Tibetan Plateau (China) have been investigated. Small subunit 16S
rRNA sequences and phylogenetic relationships have been studied for 108 bacterial isolates recovered under aerobic growth
conditions from different regions of the ice core. The genomic fingerprints based on ERIC (enterobacterial repetitive intergenic
consensus)-polymerase chain reaction and physiological heterogeneity of the closely evolutionary related bacterial strains
isolated from different ice core depths were analyzed as well. The results showed that the total microbial cell, percentages
of live cells, and the bacterial CFU ranged from 104 to 105 cell ml−1 (Mean, 9.47 × 104; SD, 5.7 × 104, n = 20), 25–81%, and 0–760 cfu ml−1, respectively. The majority of the isolates had 16S rRNA sequences similar to previously determined sequences, ranging from
92 to 99% identical to database sequences. Based on their 16S rRNA sequences, 42.6% of the isolates were high-G + C-content
(HGC) gram-positive bacteria, 35.2% were low-G + C (LGC) gram-positive bacteria, 16.6% were Proteobacteria, and 5.6% were CFB group. There were clear differences in the depth distribution of the bacterial isolates. The isolates
tested exhibited unique phenotypic properties and high genetic heterogeneity, which showed no clear correlation with depths
of bacterial isolation. This layered distribution and high heterogeneity of bacterial isolates presumably reflect the diverse
bacterial sources and the differences in bacteria inhabiting the glacier’s surface under different past climate conditions. 相似文献
15.
In this study, the collective microbial diversity in anaerobic digesters was examined using a meta-analysis approach. All 16S rRNA gene sequences recovered from anaerobic digesters available in public databases were retrieved and subjected to phylogenetic and statistical analyses. As of May 2010, 16,519 bacterial and 2869 archaeal sequences were found in GenBank. The bacterial sequences were assigned to 5926 operational taxonomic units (OTUs, based on ?97% sequence identity) representing 28 known bacterial phyla, with Proteobacteria (1590 OTUs), Firmicutes (1352 OTUs), Bacteroidetes (705 OTUs), and Chloroflexi (693 OTUs) being predominant. Archaeal sequences were assigned to 296 OTUs, primarily Methanosaeta and the uncharacterized WSA2 group. Nearly 60% of all sequences could not be classified to any established genus. Rarefaction analysis indicates that approximately 60% of bacterial and 90% of archaeal diversity in anaerobic digesters has been sampled. This analysis of the global bacterial and archaeal diversity in AD systems can guide future studies to further examine the microbial diversity involved in AD and development of comprehensive analytical tools. 相似文献
16.
Novel Rumen Bacterial Diversity in Two Geographically Separated Sub-Species of Reindeer 总被引:2,自引:0,他引:2
Svalbard reindeer (Rangifer tarandus platyrhynchus) live under austere nutritional conditions on the high-arctic archipelago of Svalbard, while semi-domesticated Norwegian
reindeer (R. tarandus tarandus) migrate between lush coastal summer pastures and inland winter pastures with lichens on mainland Norway. Svalbard reindeer
are known to have high rumen concentrations of cellulolytic bacteria, ranging from 15% of the viable population in summer
to 35% in winter, compared to only 2.5% in Norwegian reindeer. Their rumen bacterial diversity was investigated through comparative
analyses of 16S rRNA gene sequences (∼1.5 kb in length) generated from clone libraries (n = 121) and bacterial isolates (n = 51). LIBSHUFF comparisons of the composition of the two 16S rRNA libraries from Norwegian reindeer showed a significant
effect of artificial feeding compared to natural pasture, but failed to yield significant differences between libraries from
Norwegian reindeer and Svalbard reindeer. The combined sequences from reindeer were not significantly different from those
reported in wild Thompson’s gazelle in Kenya but did differ from those reported in domestic cattle in Japan. A total of 90
distinct operational taxonomic units (OTUs) were identified by employing a criterion of 97% similarity, while the Chao1 index
estimated the reindeer bacterial rumen population richness at 698 OTUs. The majority of the clone library sequences (92.5%)
represented novel strains with <97% identity to any known sequence in the public database, most of them affiliated with the
bacterial phylum Firmicutes (low G+C Gram-positives) related to the order Clostridiales (76.7%), while Gram-negative bacteria in the Bacteriodales (Prevotella–Bacteroides group) contributed to 22.5%. Also, six of the isolates were putatively novel strains, possibly representing new species in
the Clostridium subphylum (cluster XIVa), Actinomyces and Butyrivibrio. 相似文献
17.
Intestinal microflora influences many essential metabolic functions, and is receiving increasing attention from the scientific community. However, information on intestinal microbiota, especially for large wild carnivores, is insufficient. In the present study, the bacterial community in the feces of snow leopards (Uncia uncia) was described based on 16S rRNA gene sequence analysis. A total of 339 near-full-length 16S rRNA gene sequences representing 46 non-redundant bacterial phylotypes (operational taxonomical units, OTUs) were identified in fecal samples from four healthy snow leopards. Four different bacterial phyla were identified: Firmicutes (56.5 %), Actinobacteria (17.5 %), Bacteroidetes (13 %), and Proteobacteria (13 %). The phylum Actinobacteria was the most abundant lineage, with 40.4 % of all identified clones, but Clostridiales, with 50 % of all OTUs, was the most diverse bacterial order. The order Clostridiales was affiliated with four families: Clostridiaceae I, Lachnospiraceae, Peptostreptococcaceae, and Ruminococcaceae. Lachnospiraceae was the most diverse family with 17 OTUs identified. These findings were basically consistent with previous reports on the bacterial diversity in feces from other mammals. 相似文献
18.
Moez Bouali Ines Zrafi Amina Bakhrouf Sébastien Chaussonnerie Abdelghani Sghir 《Applied microbiology and biotechnology》2014,98(7):3191-3203
In this study, bacterial community structure in a horizontal subsurface flow constructed wetland (HSF-CW) planted with Phragmites australis was investigated using the 16S rRNA cloning–sequencing technique. Two layer depths were considered: the rhizosphere zone (RH) and the deep-layer zone (DL) in different sampling periods. Bacteria-specific primers 008F and 1492R were used to amplify the 16S rRNA genes and construct six clone libraries. A total of 1,284 individual sequences were used to assess the HSF-CW diversity. Phylogenetic analysis of RH and DL clone libraries shows that 41.57 and 42.17 % of the 16S rRNA sequences are affiliated with the Proteobacteria in the RH and the DL, respectively. The remaining major phylogenetic groups are Bacteroidetes, Planctomycetes, and Chloroflexi with 11.78, 9.36, and 7.6 %, respectively, in the RH and 11.38, 6.48, and 7.65 % in the DL, respectively. Minor divisions such as Verrucomicrobia, TM7, Nitrospira, and Gemmatimonadetes represented <6 % of the total sequences, while 14.2 % were unidentified Bacteria. Among the Proteobacteria, the Alphaproteobacteria subclass is represented in both locations, while the Deltaproteobacteria and Gammaproteobacteria subclasses were predominant in the RH and the DL, respectively. Results suggest that Archaea and Bacteria in the HSF-CW are the essential actors in the nitrogen cycle and that the established microbial community is efficient in nitrogen removal from wastewater. 相似文献
19.
Evidence for taxonomic and functional drift of an atrazine-degrading culture in response to high atrazine input 总被引:2,自引:0,他引:2
Udiković-Kolić N Devers-Lamrani M Petrić I Hršak D Martin-Laurent F 《Applied microbiology and biotechnology》2011,90(4):1547-1554
We evaluated the effects of variations in atrazine input on the evolution of a bacterial culture adapted to a low atrazine
concentration. This initial culture (M3-K) was subjected to weekly subculturing in the presence of a high concentration of
atrazine as the only N source (100 mg l−1). After four subculturing, M3-K evolved to a new bacterial culture (M3) which exhibited a significant increase in the extent
of atrazine mineralization in comparison with the initial culture. Molecular analyses of M3-K and M3 cultures by cloning,
restriction analysis, and sequencing of the 16S rRNA genes revealed significant differences in culture structure and composition.
M3-K culture comprised mainly Actinobacteria (40%), β-Proteobacteria (26%), and Bacteroidetes (16%). After exposure to a high atrazine concentration, the dominance of Actinobacteria decreased (14%), Bacteroidetes increased (27%), and β-Proteobacteria were replaced by γ-Proteobacteria (32%). Quantitative PCR revealed that the abundance of atzB and atzC genes relative to total bacteria decreased by a factor of 3–4 following the increase in atrazine concentration, while the
relative abundance of trzD increased significantly (≈400 times). Presented study shows that variations in atrazine input drive both functional and compositional
shifts in the atrazine-degrading bacterial culture. 相似文献
20.
A. R. Lucheta X. L. Otero F. Macías M. R. Lambais 《Extremophiles : life under extreme conditions》2013,17(6):941-951
Bacterial and archaeal community structures and diversity of three different sedimentary environments (BH1A, BH2A and BH3A) in the acid pit lake of a chalcopyrite mine at Touro (Spain) were determined by 16S rRNA gene PCR-DGGE and sequencing of clone libraries. DGGE of bacterial and archaeal amplicons showed that the sediments harbor different communities. Bacterial 16S rRNA gene sequences were assigned to Acidobacteria, Actinobacteria, Cyanobacteria, Planctomycetes, Proteobacteria, Chloroflexi and uncultured bacteria, after clustering into 42 operational taxonomic units (OTUs). OTU 2 represented approximately 37, 42 and 37 % of all sequences from sediments BH1A, BH2A and BH3A, respectively, and was phylogenetically related to uncultured Chloroflexi. Remaining OTUs were phylogenetically related to heterotrophic bacteria, including representatives of Ferrithrix and Acidobacterium genera. Archaeal 16S rRNA gene sequences were clustered into 54 OTUs. Most of the sequences from the BH1A sediment were assigned to Euryarchaeota, whereas those from BH2A sediment were assigned to Crenarchaeota. The majority of the sequences from BH3A sediment were assigned to unclassified Archaea, and showed similarities to uncultured and unclassified environmental clones. No sequences related to Acidithiobacillus and Leptospirillum, commonly associated with acid mine drainage, were detected in this study. 相似文献