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1.
Microbial community profile associated with acidic pond sediments (APS) (pH = 3·0–4·5) of freshwater finfish aquaculture ponds (n = 8) was investigated. Sediment DNA extracted from the eight APS were subjected to high-throughput sequencing of V3 and V4 regions which yielded 7236 operational taxonomic units (OTUs) at a similarity of 97%. Overall results showed higher proportion of bacterial OTUs than archaeal OTUs in all the APS. Euryarchaeota (23%), Proteobacteria (19%), Chloroflexi (17%), Crenarchaeota (5·3%), Bacteroidetes (4·8%), Nitrospirae (3·2%), Nanoarchaeaeota (3%) which together constituted 75% of the microbial diversity. At the genus level, there was high preponderance of methanogens namely Methanolinea (5·4%), Methanosaeta (4·5%) and methanotrops, Bathyarchaeota (5%) in APS. Moreover, the abundant phyla in the APS were not drastically affected by the administration of chicken slaughter waste (R-group ponds) and commercial fish feed (C-group ponds), since 67% of the OTUs generated remained common in the APS of both the groups of ponds. There was a minimal difference of 24–26% of OTUs between C-group and R-group ponds, suggesting the existence of a core microbial community in these ponds driven by acidic pH over the years. This study concludes that microbial diversity in pond sediment was influenced to a lesser extent by the addition of chicken slaughter waste but was majorly driven by acidic nature of the pond.  相似文献   

2.
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   

3.
In this study, for the first time the diversity of bacteria associated with the endemic freshwater sponge Lubomirskia baicalensis collected from the Sousern Basin of Lake Baikal was investigated employing cultivation-independent approaches. In total, 102 bacterial 16S rRNA clones were screened using restriction fragment length polymorphism (RFLP) and 30 were selected for sequencing. BLASTN and phylogenetic analysis based on near full length 16S rDNA sequences showed that 22 operational taxonomic units (OTUs) were clustered in six known phyla: Actinobacteria (8 OTUs), alpha-Proteobacteria (4 OTUs), beta-Proteobacteria (4 OTUs), Verrucomicrobia (4 OTUs), Nitrospiracea (1 OTU) and Bacteroidetes (1 OTU). Remarkably all phylotypes were affiliated to uncultured microorganisms, however, all alpha-Proteobacteria sequences were closely related to bacteria derived from the freshwater sponge Spongilla lacustris. Our results reveal a high diversity in the L. baicalensis bacterial community and provide an insight into microbial ecology and diversity within freshwater sponges inhabiting the ancient Lake Baikal ecosystem.  相似文献   

4.
Marine sponges are diverse, abundant and provide a crucial coupling point between benthic and pelagic habitats due to their high filtration rates. They also harbour extensive microbial communities, with many microbial phylotypes found exclusively in sponge hosts and not in the seawater or surrounding environment, i.e. so‐called sponge‐specific clusters (SCs) or sponge‐ and coral‐specific clusters (SCCs). We employed DNA (16S rRNA gene) and RNA (16S rRNA)‐based amplicon pyrosequencing to investigate the effects of sublethal thermal stress on the bacterial biosphere of the Great Barrier Reef sponge Rhopaloeides odorabile. A total of 8381 operational taxonomic units (OTUs) (97% sequence similarity) were identified, affiliated with 32 bacterial phyla from seawater samples, 23 bacterial phyla from sponge DNA extracts and 18 bacterial phyla from sponge RNA extracts. Sublethal thermal stress (31°C) had no effect on the present and/or active portions of the R. odorabile bacterial community but a shift in the bacterial assemblage was observed in necrotic sponges. Over two‐thirds of DNA and RNA sequences could be assigned to previously defined SCs/SCCs in healthy sponges whereas only 12% of reads from necrotic sponges could be assigned to SCs/SCCs. A rapid decline in host health over a 1°C temperature increment suggests that sponges such as R. odorabile may be highly vulnerable to the effects of global climate change.  相似文献   

5.
Mining negatively affects the environment by producing large quantities of metallic tailings, such as those contaminated with arsenic, with harmful consequences for human and aquatic life. A culture-independent molecular analysis was performed to assess the prokaryotic diversity and community structural changes of the tropical historically metal-contaminated Mina stream (MS) and the relatively pristine Mutuca stream (MTS) sediments. A total of 234 bacterial operational taxonomic units (OTUs) were affiliated with 14 (MS) and 17 (MTS) phyla and 53 OTUs were associated with two archaeal phyla. Although the bacterial community compositions of these sediments were markedly distinct, no significant difference in the diversity indices between the bacterial communities was observed. Additionally, the rarefaction and diversity indices indicated a higher bacterial diversity than archaeal diversity. Most of the OTUs were affiliated with the Proteobacteria and Bacteroidetes phyla. Alphaproteobacteria, Gemmatimonadetes and Actinobacteria were only found in the MS clone library. Crenarchaeal 16S rDNA sequences constituted 75 % of the MS archaeal clones, whereas Euryarchaeota were dominant in the MTS clones. Despite the markedly different characteristics of these streams, their bacterial communities harbor high diversity, suggesting that historically mining-impacted sediments promote diversity. The findings also provide basis for further investigation of members of Alphaproteobacteria as potential biological indicators of arsenic-rich sediments.  相似文献   

6.
The aim of this study was to describe the microbial communities in the distal gut of wild wolves (Canis lupus). Fecal samples were collected from three healthy unrelated adult wolves captured at the nearby of Dalai Lake Nature Reserve in Inner Mongolia of China. The diversity of fecal bacteria was investigated by constructing PCR-amplified 16S rRNA gene clone libraries using the universal bacterial primers 27 F and 1493 R. A total of 307 non-chimeric near-full-length 16S rRNA gene sequences were analyzed and 65 non-redundant bacteria phylotypes (operational taxonomical units, OTUs) were identified. Seventeen OTUs (26%) showed less than 98% sequence similarity to 16S rRNA gene sequences were reported previously. Five different bacterial phyla were identified, with the majority of OTUs being classified within the phylum Firmicutes (60%), followed by Bacteroidetes (16.9%), Proteobacteria (9.2%), Fusobacteria (9.2%) and Actinobacteria (4.6%). The majority of clones fell within the order Clostridiales (53.8% of OTUs). It was predominantly affiliated with five families: Lachnospiraceae was the most diverse bacterial family in this order, followed by Ruminococcaceae, Clostridiaceae, Peptococcaceae and Peptostreptococcaceae.  相似文献   

7.
海水循环水养殖系统是重要的生态养殖模式发展趋势之一, 为了深入了解循环水养殖生态系统, 通过对系统各功能区水体中细菌16S rRNA基因V4V5区进行高通量测序和生物信息学分析, 从微生物生态学角度分析了循环水养殖系统不同功能区的细菌群落结构动态。测序分析结果显示, 海水循环水养殖系统中优势细菌种群分别属于变形菌门(Proteobacteria)、蓝藻门(Cyanobacteria)、拟杆菌门(Bacteroidetes)、厚壁菌门(Firmicutes)、放线菌门(Actinobacteria)和浮霉菌门(Planctomycetes)。红树林湿地水体中变形菌门和厚壁菌门丰度较高, 而对虾养殖池的拟杆菌门和浮霉菌门丰度较高。在不同优势类群中, 变形菌门多样性指数平均值最高, 其次是拟杆菌门, 厚壁菌门最低。在各功能区中, 红树林细菌多样性最高, 虾池最低。MDS分析结果显示虾池、贝池和红树林湿地水体中细菌群落结构有明显差异, 虾池与其他功能区差异最大。研究表明, 高密度对虾养殖对虾池水体中细菌群落有显著影响, 但其影响在循环水养殖系统后续功能区中逐渐减弱。  相似文献   

8.
温彬  高勤峰  董双林  宁鲁光 《生态学报》2016,36(14):4327-4336
于2012年7月至2013年4月调查了荣成靖海湾3个不同水深的刺参(Apostichopus japonicus)养殖池塘内大型底栖动物的构成,以了解不同水深对刺参养殖池塘环境条件的影响以及由此引起的大型底栖生物群落结构的改变。结果表明:3个不同水深梯度池塘(1#浅水位、2#正常水位和3#高水位)底部光照强度、叶绿素a(Chla)和总有机物(TOM)含量存在显著差异,各池塘水温差异不显著。光强、Chla和TOM含量在夏季、冬季和春季均表现为1#池塘显著高于3#池塘;秋季各池塘间光强和TOM含量差异不显著,Chla含量则表现为3#池塘显著高于1#池塘。各季节3个池塘间大型底栖动物在种类组成、丰度、生物量和多样性指数上均存在显著性差异。大型底栖动物丰度和生物量夏季均表现为1#池塘显著高于3#池塘,秋季和冬季则相反;春季1#池塘丰度显著高于3#池塘,生物量则差异不显著。这些差异主要与其各自优势种及其优势度指数大小有关。大型底栖动物多样性指数夏季和秋季均表现为1#池塘高于3#池塘,春季则相反,冬季各池塘间多样性指数差异不显著。单因子相似性分析(ANOSIM)表明,各季节3个池塘间大型底栖动物群落结构均存在显著差异,表明水深梯度对刺参养殖池塘大型底栖动物群落结构造成显著性影响。相似性百分比分析(SIMPER)显示,各季节对3个池塘间大型底栖动物群落差异起主要作用的物种为各个池塘的优势种。典范对应分析(CCA)表明,水深、Chla和TOM含量为影响大型底栖动物群落的主要环境因子。  相似文献   

9.
A culture-independent molecular phylogenetic approach was used to study prokaryotic diversity in an anoxic activated sludge from a municipal wastewater treatment plant. Two 16S rRNA gene libraries were constructed using total genomic DNA and amplified by polymerase chain reaction using primers specific for archaeal or bacterial domains. Phylogenetic analysis of 132 and 249 almost full-length 16S rRNA genes for Archaea and Bacteria, respectively, was done using the ARB software package. Phylogenetic groups affiliated with the Archaea belong to Euryarchaeota (93.8% of the operational taxonomic units [OTUs]) and Crenarchaeota (6.2% of the OTUs). Within the bacterial library, 84.8% of the OTUs represent novel putative phylotypes never described before and affiliated with ten divisions. The Proteobacteria phylum is the most abundant and diversified phylogenetic group representing 60.4% of the OTUs, followed by Bacteroidetes (22.1%) and gram-positives (6.1%). Interestingly, we detected a novel Proteobacteria monophyletic group distinct from the five known subclasses, which we named New Lineage of Proteobacteria (NLP) lineage, and it is composed of eight clones representing 4.6% of the Proteobacteria. A new 16S rRNA-targeted hybridization probe was designed and fluorescent in situ hybridization analyses shows representatives of NLP as cocci-shaped microorganisms. The Chloroflexi, Acidobacterium, and Nitrospira phyla and TM7 candidate division are each represented by ≤3% of clone sequences. A comprehensive set of eight 16S and 23S rRNA-targeted oligonucleotide probes was used to quantify these major groups by dot blot hybridization within 12 samples. The Proteobacteria accounted for 82.5 ± 4.9%, representing the most abundant phyla. The Bacteroidetes and Planctomycetales groups accounted for 4.9 ± 1.3% and 4 ± 1.7%, respectively. Firmicutes and Actinobacteria together accounted for only 1.9 ± 0.5%. The set of probes covers 93.4 ± 14% of the total bacterial population rRNA within the anoxic basin.  相似文献   

10.
沙月霞 《微生物学报》2018,58(12):2216-2228
[目的]为详细了解水稻不同组织内生细菌群落多样性。[方法]对宁粳43号内生细菌的总DNA提取后,采用高通量测序技术对水稻内生细菌的16S rRNA基因进行了序列测定,分析了水稻不同组织部位内生细菌群落结构特征。[结果]叶部共获得内生细菌OTUs 610个,茎部411个,根部174个。物种分类显示,叶部内生细菌种类隶属于22门40纲103目198科399属,其中优势类群是红球菌属(Rhodococcus)和乳酸杆菌属(Lactobacillus),它们的相对丰度分别为21.00%和9.19%;茎部内生细菌种类隶属于19门31纲85目169科306属,其中优势类群是红球菌属和罗尔斯通菌属(Ralstonia),它们的相对丰度分别为19.25%和13.52%;根部内生细菌种类隶属于9门19纲44目82科140属,其中优势类群是肠杆菌属(Enterobacter)和埃希氏杆菌属(Escherichia),它们的相对丰度分别为81.13%和10.89%。根茎叶中相同的OTU有78个,放线菌门(Actinobacteria)与大多数细菌具有相关性。根系内生细菌中具有调控各种代谢网络功能的物种丰度高于茎部和叶部。[结论]不同水稻组织内生细菌具有丰富的群落多样性,其中叶部的内生细菌物种最丰富,根系参与各种代谢调控的细菌丰度最高,各个组织部位的优势菌属各不相同,变形菌门是最重要的水稻内生细菌。  相似文献   

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