Prokaryotic metabolic activity and community structure in Antarctic continental shelf sediments

The prokaryote community activity and structural characteristics within marine sediment sampled across a continental shelf area located off eastern Antarctica (66 degrees S, 143 degrees E; depth range, 709 to 964 m) were studied. Correlations were found between microbial biomass and aminopeptidase and chitinase rates, which were used as proxies for microbial activity. Biomass and activity were maximal within the 0- to 3-cm depth range and declined rapidly with sediment depths below 5 cm. Most-probable-number counting using a dilute carbohydrate-containing medium recovered 1.7 to 3.8% of the sediment total bacterial count, with mostly facultatively anaerobic psychrophiles cultured. The median optimal growth temperature for the sediment isolates was 15 degrees C. Many of the isolates identified belonged to genera characteristic of deep-sea habitats, although most appear to be novel species. Phospholipid fatty acid (PLFA) and isoprenoid glycerol dialkyl glycerol tetraether analyses indicated that the samples contained lipid components typical of marine sediments, with profiles varying little between samples at the same depth; however, significant differences in PLFA profiles were found between depths of 0 to 1 cm and 13 to 15 cm, reflecting the presence of a different microbial community. Denaturing gradient gel electrophoresis (DGGE) analysis of amplified bacterial 16S rRNA genes revealed that between samples and across sediment core depths of 1 to 4 cm, the community structure appeared homogenous; however, principal-component analysis of DGGE patterns revealed that at greater sediment depths, successional shifts in community structure were evident. Sequencing of DGGE bands and rRNA probe hybridization analysis revealed that the major community members belonged to delta proteobacteria, putative sulfide oxidizers of the gamma proteobacteria, Flavobacteria, Planctomycetales, and Archaea. rRNA hybridization analyses also indicated that these groups were present at similar levels in the top layer across the shelf region.     

Prokaryotic Metabolic Activity and Community Structure in Antarctic Continental Shelf Sediments

The prokaryote community activity and structural characteristics within marine sediment sampled across a continental shelf area located off eastern Antarctica (66°S, 143°E; depth range, 709 to 964 m) were studied. Correlations were found between microbial biomass and aminopeptidase and chitinase rates, which were used as proxies for microbial activity. Biomass and activity were maximal within the 0- to 3-cm depth range and declined rapidly with sediment depths below 5 cm. Most-probable-number counting using a dilute carbohydrate-containing medium recovered 1.7 to 3.8% of the sediment total bacterial count, with mostly facultatively anaerobic psychrophiles cultured. The median optimal growth temperature for the sediment isolates was 15°C. Many of the isolates identified belonged to genera characteristic of deep-sea habitats, although most appear to be novel species. Phospholipid fatty acid (PLFA) and isoprenoid glycerol dialkyl glycerol tetraether analyses indicated that the samples contained lipid components typical of marine sediments, with profiles varying little between samples at the same depth; however, significant differences in PLFA profiles were found between depths of 0 to 1 cm and 13 to 15 cm, reflecting the presence of a different microbial community. Denaturing gradient gel electrophoresis (DGGE) analysis of amplified bacterial 16S rRNA genes revealed that between samples and across sediment core depths of 1 to 4 cm, the community structure appeared homogenous; however, principal-component analysis of DGGE patterns revealed that at greater sediment depths, successional shifts in community structure were evident. Sequencing of DGGE bands and rRNA probe hybridization analysis revealed that the major community members belonged to delta proteobacteria, putative sulfide oxidizers of the gamma proteobacteria, Flavobacteria, Planctomycetales, and Archaea. rRNA hybridization analyses also indicated that these groups were present at similar levels in the top layer across the shelf region.     

Insights into Diversity and Imputed Metabolic Potential of Bacterial Communities in the Continental Shelf of Agatti Island

Marine microbes play a key role and contribute largely to the global biogeochemical cycles. This study aims to explore microbial diversity from one such ecological hotspot, the continental shelf of Agatti Island. Sediment samples from various depths of the continental shelf were analyzed for bacterial diversity using deep sequencing technology along with the culturable approach. Additionally, imputed metagenomic approach was carried out to understand the functional aspects of microbial community especially for microbial genes important in nutrient uptake, survival and biogeochemical cycling in the marine environment. Using culturable approach, 28 bacterial strains representing 9 genera were isolated from various depths of continental shelf. The microbial community structure throughout the samples was dominated by phylum Proteobacteria and harbored various bacterioplanktons as well. Significant differences were observed in bacterial diversity within a short region of the continental shelf (1–40 meters) i.e. between upper continental shelf samples (UCS) with lesser depths (i.e. 1–20 meters) and lower continental shelf samples (LCS) with greater depths (i.e. 25–40 meters). By using imputed metagenomic approach, this study also discusses several adaptive mechanisms which enable microbes to survive in nutritionally deprived conditions, and also help to understand the influence of nutrition availability on bacterial diversity.     

Diversity of bacteria associated with Bursaphelenchus xylophilus and other nematodes isolated from Pinus pinaster trees with pine wilt disease

The pinewood nematode (PWN), Bursaphelenchus xylophilus, has been thought to be the only causal agent of pine wilt disease (PWD), however, since bacteria have been suggested to play a role in PWD, it is important to know the diversity of the microbial community associated to it. This study aimed to assess the microbial community associated with B. xylophilus and with other nematodes isolated from pine trees, Pinus pinaster, with PWD from three different affected forest areas in Portugal. One hundred and twenty three bacteria strains were isolated from PWN and other nematodes collected from 14 P. pinaster. The bacteria strains were identified by comparative analysis of the 16S rRNA gene partial sequence. All except one gram-positive strain (Actinobacteria) belonged to the gram-negative Beta and Gammaproteobacteria. Most isolates belonged to the genus Pseudomonas, Burkholderia and to the family Enterobacteriaceae. Species isolated in higher percentage were Pseudomonas lutea, Yersinia intermedia and Burkholderia tuberum. The major bacterial population associated to the nematodes differed according to the forest area and none of the isolated bacterial species was found in all different forest areas. For each of the sampled areas, 60 to 100% of the isolates produced siderophores and at least 40% produced lipases. The ability to produce siderophores and lipases by most isolates enables these bacteria to have a role in plant physiological response. This research showed a high diversity of the microbial community associated with B. xylophilus and other nematodes isolated from P. pinaster with PWD.     

Characterization of depth-related population variation in microbial communities of a coastal marine sediment using 16S rDNA-based approaches and quinone profiling

Depth-related changes in whole-community structure were evaluated in a coastal marine sediment using a molecular fingerprinting method, terminal restriction fragment length polymorphism (T-RFLP) analysis, and a chemotaxonomic technique (quinone profiling). Dendrograms derived from both T-RFLP analysis and quinone profiling indicated a significant variation in microbial community structure between the 0-2 cm layer and deeper layers. This corresponded to the dramatic change in the redox potential, acid-volatile sulphide-sulphur and bacterial numbers observed at 0-2 cm and 2-4 cm depths. A significant change in the number of terminal restriction fragments (T-RFs) was also detected at this transition depth. However, the change in major T-RFs with depth was not seen in electropherograms. The population changes were primarily variations in minor ribotypes. Most quinone homologues were detected at all depths, although the quinone composition changed with depth. Therefore, quinone profiling also suggested that the depth-related variation was primarily attributable to minor bacterial groups rather than change in the major population structure. 16S rDNA clone library analysis revealed that clones belonging to the genera Vibrio and Serratia predominated as major bacterial groups at all depths. Our data suggested that the sediment community might result from sedimentation effects of sinking particles. Overall, our results demonstrated that the combined methods of T-RFLP analysis and quinone profiling were effective for assessing depth-related microbial populations.     

Phylogenetic diversity of culturable bacteria from Antarctic sandy intertidal sediments

The diversity of culturable bacteria associated with sandy intertidal sediments from the coastal regions of the Chinese Antarctic Zhongshan Station on the Larsemann Hills (Princess Elizabeth Land, East Antarctica) was investigated. A total of 65 aerobic heterotrophic bacterial strains were isolated at 4°C. Microscopy and 16S rRNA gene sequence analysis indicated that the isolates were dominated by Gram-negative bacteria, while only 16 Gram-positive strains were isolated. The bacterial isolates fell in five phylogenetic groups: Alpha- and Gammaproteobacteria, Bacteroidetes, Actinobacteria and Firmicutes. Based on phylogenetic trees, all the 65 isolates were sorted into 29 main clusters, corresponding to at least 29 different genera. Based on sequence analysis (<98% sequence similarity), the Antarctic isolates belonged to at least 37 different bacterial species, and 14 of the 37 bacterial species (37.8%) represented potentially novel taxa. These results indicated a high culturable diversity within the bacterial community of the Antarctic sandy intertidal sediments.     

Psychrotrophic bacteria from a coastal station in the Ross sea (Terra Nova Bay, Antarctica).

Seawater samples were collected from a fixed, coastal station in the Terra Nova Bay at different depths during the Xth Oceanographic Cruise in the 1994-95 Antarctic summer. Picoplanktonic abundance, estimated by direct counts in epifluorescence microscopy, ranged from 2.2 x 10(7) to 1.6 x 10(8) cells.l-1. The heterotrophic bacterial densities, evaluated on Marine Agar 2216 (Difco) after incubation at +4 degrees C for 21 days, ranged from 2 x 10(3) to 4.5 x 10(6) CFU.l-1. The qualitative composition of the heterotrophic bacterial community was studied on 64 morphological and biochemical characters of the 125 strains isolated. Heterotrophic, psychrotrophic isolates were tentatively identified at genus level as Pseudomonas, Vibrio, Acinetobacter, and Flavobacterium/Cytophaga. In order to compare the characteristics of the isolates with those previously studied during 1989/90, the synthetical indices of the structure and the metabolic potentiality of the heterotrophic bacterial community were processed. Results showed that the bacterial community was metabolically more active and more homogenous than that previously studied.     

Genetic and phenotypic diversity of plant growth promoting rhizobacteria isolated from sugarcane plants growing in pakistan

Bacteria were isolated from roots of sugarcane varieties grown in the fields of Punjab. They were identified by using API20E/NE bacterial identification kits and from sequences of 16S rRNA and amplicons of the cpn60 gene. The majority of bacteria were found to belong to the genera of Enterobacter, Pseudomonas, and Klebsiella, but members of genera Azospirillum, Rhizobium, Rahnella, Delftia, Caulobacter, Pannonibacter, Xanthomonas, and Stenotrophomonas were also found. The community, however, was dominated by members of the Pseudomonadaceae and Enterobacteriaceae, as representatives of these genera were found in samples from every variety and location examined. All isolates were tested for the presence of five enzymes and seven factors known to be associated with plant growth promotion. Ten isolates showed lipase activity and eight were positive for protease activity. Cellulase, chitinase, and pectinase were not detected in any strain. Nine strains showed nitrogen fixing ability (acetylene reduction assay) and 26 were capable of solubilizing phosphate. In the presence of 100 mg/l tryptophan, all strains except one produced indole acetic acid in the growth medium. All isolates were positive for ACC deaminase activity. Six strains produced homoserine lactones and three produced HCN and hexamate type siderophores. One isolate was capable of inhibiting the growth of 24 pathogenic fungal strains of Colletotrichum, Fusarium, Pythium, and Rhizoctonia spp. In tests of their abilities to grow under a range of temperature, pH, and NaCl concentrations, all isolates grew well on plates with 3% NaCl and most of them grew well at 4 to 41degrees C and at pH 11.     

Effect of natamycin on the enumeration, genetic structure and composition of bacterial community isolated from soils and soybean rhizosphere

Natamycin is commonly used to control fungal growth on agar media used for bacterial enumeration or strain isolation. However, there is no conclusive report on the possible effect of this antibiotic on bacterial growth or on the diversity of the recovered soil bacteria. Therefore, the possible effects of natamycin on the numbers of bacteria isolated at 12 degrees C from three different soils and soybean rhizosphere soil were investigated using natamycin concentrations ranging from 0 to 200 mg l(-1). Our results demonstrate that natamycin concentrations, which inhibit the growth of fungi on the media, have a small but significant inhibitory effect on the number of bacterial colony forming units. A natamycin concentration of 50-200 mg l(-1) is required for an efficient control of fungal growth on media in our experimental conditions depending on the soil type. Bacterial community structure was assessed on culturable cells (cells washed from enumeration plates: plate-wash approach) obtained at 12 degrees C from soybean rhizosphere soil by performing Ribosomal Intergenic Spacer Analysis (RISA) fingerprinting. We demonstrate that all natamycin concentrations used alter the structure of the recovered, culturable bacterial community, compared to control without natamycin. Using ARDRA (amplification of the 16S rDNA gene and restriction analysis) genotyping of individual isolates, some differences were observed between the bacterial isolates obtained in the presence or absence of natamycin. Bacterial isolates recovered in the presence of natamycin are more tolerant (maximal growth rate and lag phase) to this compound than those isolated without natamycin, indicating a possible selection of resistant strains. Therefore, high concentration of natamycin cannot be used for isolation of bacterial strains with the aim of studying biodiversity and could bias a selection of strains for practical applications.     

Diversity and physiology of culturable bacteria associated with a coastal Antarctic ice core

Microbiological studies of polar ice at different depths may provide important comparisons, as they preserve records of microbial cells and past climate. In this study, we examined bacterial abundance, diversity and glaciochemical composition from three depths of an ice core from coastal Dronning Maud Land, East Antarctica. Higher bacterial abundance corresponded with high in situ sea-salt Na(+) and dust concentration, suggesting that bacteria might have been transported and deposited into ice along with dust particles and marine aerosols. Fourteen bacterial isolates belonging to the genera Methylobacterium, Brevundimonas, Paenibacillus, Bacillus and Micrococcus were retrieved. Frequent isolation of similar bacterial genera from different cold environments suggests that they possess features that enable survival and metabolism for extended periods of time at sub-zero temperatures. The highest number and diversity of recoverable bacteria was obtained from 49 m depth corresponding to 1926 AD and consisted of bacteria from 4 different genera whereas at 11 m (1989 AD) and 33 m (1953 AD) samples only species belonging to the genera Bacillus was recovered. Among the Bacillus species, Bacillus aryabhattai which has been reported only from the upper stratosphere, was isolated and is the first record from the Earth's surface. Methylobacterium was the most dominant genera at 49 m depth and its prevalence is attributable to a combination of high in situ methanesulfonate concentration, specialized metabolism and environmental hardiness of Methylobacterium. Some of the isolated bacteria were found to respire and grow using methanesulfonate, suggesting that they may utilize this substrate to sustain growth in ice. In addition, NO(3)(-) (2.93-3.69 μM), NH(4)(+) (1.45-3.90 μM) and PO(4)(3-) (0.01-0.75 μM) present in the ice could be potential sources fueling bacterial metabolism in this environment. It could be deduced from the study that variation in bacterial abundance and diversity was probably associated with the prevailing in situ conditions in ice.     

Production of quorum-sensing-related signal molecules by epiphytic bacteria inhabiting wheat heads

The production of quorum-sensing-related signal molecules (QSRMs) among culturable bacteria comprising the community on wheat heads was investigated. The taxonomic position of 186 bacterial isolates obtained from ten heads was inferred based on 16S rRNA gene sequences, and their QSRM production was determined using two bioreporter strains of N-acylhomoserine lactones. Approximately 33% of isolates produced QSRMs, though the proportion of QSRM-producing isolates on a wheat head was significantly negatively correlated with population size. Most of the producing isolates were Pantoea species, most commonly Pantoea ananatis. Furthermore, the proportion of Pantoea ananatis that produced QSRMs was significantly negatively correlated with the number of bacterial genera (community richness) on each head. Finally, community richness was positively correlated with population size. Qualitative analysis using thin-layer-chromatography revealed that the QSRMs of Pantoea isolates were composed of at least two compounds. This is the first report indicating that Pantoea ananatis isolates inhabiting wheat heads are capable of producing QSRMs. QSRM production by Pantoea spp. may contribute to the predominance of this genus on wheat heads, particularly at relatively low population densities and community diversity.     

Response of microbial community structure to natural and accelerated hydrarch successions in the boreal wetlands in northern Hokkaido, Japan

We estimated the effect of invading Sasa vegetation and accelerated terrestrialization on the microbial community structure in Sarobetsu-genya wetland (SGW) and Nakanominedaira wetland (NW) (original vegetation, Sphagnum). All examined peat-pore water samples were acidic. Electrical conductivity significantly differed between SGW and NW. Nonmetric multidimensional scaling (NMDS) and analysis of similarity based on denaturing gradient gel electrophoresis (DGGE) band patterns revealed differences in the bacterial community structure between the Sasa and Sphagnum vegetations at a depth of 10 cm in NW. In contrast, the bacterial NMDS profiles at all depths differed between the 2 wetlands rather than between the 2 vegetations. The archaeal community structure significantly differed between the wetlands at depths of 30 and 50 cm. The bacterial diversity index derived from the DGGE profiles significantly differed between the wetlands at all depths. The archaeal diversity index significantly differed between the wetlands at a depth of 50 cm. Sasa invasion affected the microbial community structure in the rhizosphere, up to a depth of 10 cm; this effect differed with the terrestrialization speed. These results suggest that in peat bogs subjected to artificially accelerated terrestrialization, the microbial community changes before the occurrence of the natural hydrarch ecological succession involving ground vegetation.     

Novel P-Solubilizers from Calcium Bound Phosphate Rich Pine Forest of Lower Himalaya

Phosphorus, an essential element for life, is continuously depleting from soils and thus demands sustainable management particularly in agriculture and forestry. Inorganic P constitutes the major proportion as tricalcium phosphate in soils of lower Himalayan region of Pakistan. We sampled these soils and screened for P-solubilizing microbes. A range of culturable microbial community (bacteria and fungi) was isolated and molecularly characterized which make the P available from mineral phosphates. There was an increase in abundance of phosphate solubilizing bacteria (PSB) at a 6-inch depth of the pine rhizosphere compared to the surface soil samples. Moreover, the isolates from lower Himalaya have higher abundance and better efficiency to solubilize the inorganic P than the ones from non-Himalaya. Most likely the P-solubilization done by our P-solubilizing microbes is via acidification as we observed the decrease in pH of the medium of microbial growth. Furthermore, the majority of isolated PSB belong to gammaproteobacterial class of Gram negative bacteria. Most interestingly, 13% of our isolated PSB were psychrotolerant (physiologically active at cold environment, i.e., 4°C) and able to solubilize inorganic P as efficiently as at ambient temperature. This study is unique in reporting the P-solubilizing microbes, particularly the psychrotolerant bacterial strains, of Lower Himalaya. Therefore the isolated bacterial and fungal strains have potential and may serve as biofertilizers in the region to increase the P availability in soils.     

构树可培养内生真菌的多样性初探

构树Broussonetia papyrifera为桑科重要的资源植物。为调查逆境构树内生真菌的多样性,我们对铅锌矿区构树根、茎、叶和果实各部位进行内生真菌分离鉴定,从中分离得到187株内生真菌,根据形态学与分子生物学方法鉴定为20属,其中链格孢属Alternaria（50.27%）、镰孢属Fusarium（11.76%）为优势属。不同培养基的内生真菌分离率结果表明,马铃薯葡萄糖琼脂培养基（PDA）分离出的菌株数最多,占总数的73.96%;构树不同部位的菌株分离数目显示,叶中分离出的菌株较多,占38.02%。在属的分类水平上,根、茎、叶、果实不同部位的真菌数量也存在明显差异。Shannon-Wiener多样性指数和Simpson多样性指数分析结果提示不同样地的构树内生真菌的多样性也存在差异。Chao1指数和ACE指数也提示构树内生真菌丰富度与样地和组织有关。     

Diversity of N-acyl homoserine lactone-producing and -degrading bacteria in soil and tobacco rhizosphere

In Gram-negative bacteria, quorum-sensing (QS) communication is mostly mediated by N-acyl homoserine lactones (N-AHSL). The diversity of bacterial populations that produce or inactivate the N-AHSL signal in soil and tobacco rhizosphere was investigated by restriction fragment length polymorphism (RFLP) analysis of amplified 16S DNA and DNA sequencing. Such analysis indicated the occurrence of N-AHSL-producing strains among the alpha-, beta- and gamma-proteobacteria, including genera known to produce N-AHSL (Rhizobium, Sinorhizobium and Pseudomonas) and novel genera with no previously identified N-AHSL-producing isolates (Variovorax, Sphingomonas and Massilia). The diversity of N-AHSL signals was also investigated in relation to the genetic diversity of the isolates. However, N-AHSL-degrading strains isolated from soil samples belonged to the Bacillus genus, while strains isolated from tobacco rhizospheres belonged to both the Bacillus genus and to the alpha subgroup of proteobacteria, suggesting that diversity of N-AHSL-degrading strains may be modulated by the presence of the tobacco plant. Among these rhizospheric isolates, novel N-AHSL-degrading genera have been identified (Sphingomonas and Bosea). As the first simultaneous analysis of both N-AHSL-degrading and -producing bacterial communities in a complex environment, this study revealed the coexistence of bacterial isolates, belonging to the same genus or species that may produce or degrade N-AHSL.     

秦岭地区野生细鳞鲑肠道微生物多样性及产酶活性分析

为探究秦岭地区野生细鳞鲑(Brachymystax lenok)肠道细菌组成多样性,筛选出产胞外酶菌株,利用传统分离培养并分子鉴定的方法和基于16S r RNA基因克隆的现代分子生物技术相结合测定秦岭野生细鳞鲑肠道细菌菌群多样性并构建系统发育树,利用淀粉酶、蛋白酶、纤维素酶及脂肪酶4种胞外酶筛选培养基筛选出产上述酶的细菌。细菌传统分离培养并分子鉴定法从细鳞鲑肠道获得18个属的细菌类群,分别归属于变形菌门、拟杆菌门和厚壁菌门,其中,气单胞菌属(Aeromonas)为优势菌群。基于16S r RNA基因克隆的现代分子方法获得22个属的细菌类群,分别归属于变形菌门、拟杆菌门、厚壁菌门和放线菌门,其中,鞘氨醇杆菌属(Sphingomonas)为优势菌群。4种胞外酶筛选获得53株细菌产胞外酶,其中21株可在低温(10℃)环境下产胞外酶。结果表明,传统分离培养法与基于16S r RNA基因克隆的现代分子生物技术相结合能够更有效全面地分析细鳞鲑鱼肠道微生物的多样性,并且细鳞鲑肠道微生物具有一定的产酶活性。     

Application of fluorescence internal transcribed spacer-PCR (f-ITS) for the cluster analysis of bacteria isolated from air and deteriorated fresco surfaces

The aim of this work was the evaluation of fluorescence ITS-PCR (f-ITS) as a molecular tool to analyze the microbial community involved in the biodeterioration of cultural heritage surfaces. As a case study we analyzed by f-ITS ninety-two bacterial strains isolated from a medieval fresco and the surrounding air environment. The internal transcribed spacer between the 16S and 23S rRNA genes was amplified, and then the fluorescently labeled PCR products were separated by capillary electrophoresis. Bacterial strains were identified by 16S rDNA sequencing. The f-ITS electropherograms showed different profiles coherent with the affiliation of the strains at the genus and species levels. Among the isolates obtained from the fresco surface, those belonging to the genus Bacillus were the most prevailing exhibiting 8 different f-ITS profiles. The airborne bacilli exhibited only 2 of these 8 profiles. Staphylococcus were mostly isolated from air and produced 4 different profiles. Pseudomonas isolates presented 3 different profiles, and one of them was typical of Pseudomonas putida. Members of the other genera produced their distinctive profiles. Our results show that f-ITS is a promising molecular tool for the rapid selection and clustering of strains isolated from different sources.     

Bacteria associated with orchid roots and microbial production of auxin

Associative bacteria of terrestrial (Paphiopedilum appletonianum) and epiphytic (Pholidota articulata) tropical orchids were investigated. Microbial community of epiphytic plant differed from that of the terrestrial one. Streptomyces, Bacillus, Pseudomonas, Burkholderia, Erwinia and Nocardia strains populated Paphiopedilum roots, whereas Pseudomonas, Flavobacterium, Stenotrophomonas, Pantoea, Chryseobacterium, Bacillus, Agrobacterium, Erwinia, Burkholderia and Paracoccus strains colonized Pholidota roots. Endophytic bacteria populations were represented with less diversity: Streptomyces, Bacillus, Erwinia and Pseudomonas genera were isolated from P. appletonianum, and Pseudomonas, Bacillus, and Flavobacterium genera were isolated from Ph. articulata. Microorganisms produced indole-3-acetic acid (IAA). Variations in its biosynthesis among the strains of the same genus were also observed. The highest auxin level was detected during the stationary growth phase. Biological activity of microbial IAA was proved by treatment of kidney bean cuttings with bacterial supernatants, revealing considerable stimulation of root formation and growth.     

织金洞钟乳石沉积物表面可培养细菌多样性和网络分析

【背景】洞穴环境中蕴含丰富而独特的细菌资源,对洞穴环境中细菌的分离培养有助于了解洞穴细菌多样性及细菌资源的挖掘和利用。【目的】利用不同培养基分离细菌,探究钟乳石表面可培养细菌的多样性及其种间互作关系。【方法】通过11种培养基对织金洞内钟乳石沉积物表面的细菌进行分离纯化,并利用16S rRNA基因序列分析初步确定分离菌株的分类地位。在R软件下,通过Bipartite包分析可培养细菌属间的相互作用。【结果】从钟乳石沉积物表面共分离出206株细菌,它们隶属于4门25属45种,香农(Shannon)指数为4.78,辛普森(Simpson)指数为0.95。变形菌门(Proteobacteria)和芽孢杆菌属(Bacillus)分别为样品中可培养细菌的优势门(47.09%)和优势属(29.61%)。无机寡营养培养基有助于洞穴钟乳石沉积物细菌的分离。属水平-采样点网络分析表明,可培养细菌分布具有非随机、显著的嵌套性。芽孢杆菌属(Bacillus)、德沃斯氏菌属(Devosia)、产碱杆菌属(Alcaligenes)、节杆菌属(Arthrobacter)和短杆菌属(Brevibacterium)在细菌群落中存在较多的有效合作值(Effective Partners)和亲密度(Closeness),被其他细菌所依赖程度(Species Strength)较高,是该群落中的重要组成类群。【结论】织金洞内钟乳石沉积物表面存在丰富的细菌资源,分析细菌类群在群落中的作用应结合细菌相对丰度和网络分析。     

沙埋对干旱沙区真藓结皮层细菌群落结构和多样性的影响

作为干旱沙区常见干扰之一的沙埋显著影响着生物结皮的结构和功能,但其内在的生物学机理还不清楚。利用高通量测序技术,通过对0(对照)、0.5(浅层)、2和10mm(深层)沙埋处理后的腾格里沙漠东南缘沙坡头地区真藓(Bryum argenteum)结皮层细菌群落物种组成与丰度的测定,研究了沙埋对真藓结皮层细菌群落结构和多样性的影响。结果表明:(1)共检测到沙坡头地区真藓结皮层细菌38门106纲181属,以放线菌、变形菌、蓝藻、浮霉菌、拟杆菌和酸杆菌等为主(占细菌群落的78.4%—83.0%);(2)PCA分析表明沙埋导致该地区真藓结皮层细菌群落结构组成发生明显改变。无沙埋时,真藓结皮层细菌群落中相对丰度最高的是蓝藻(18.6%),随着沙埋厚度的增加,依次变为变形菌(21.5%,沙埋厚度0.5mm)、浮霉菌(21.5%,沙埋厚度2mm)和放线菌(23.3%,沙埋厚度10mm);浅层沙埋显著增加了真藓结皮层细菌群落中光合菌、固氮菌和产菌丝体细菌等关键功能菌的丰度,但深层沙埋降低了它们的丰度;(3)沙埋显著增加了真藓结皮层细菌群落多样性(P0.05)和物种丰富度(P0.05),0.5mm沙埋后的细菌群落丰富度指数最高,2mm沙埋后的结皮层细菌群落多样性指数最高。揭示了沙埋对干旱沙区真藓结皮层细菌群落结构与多样性的影响,为深入理解沙埋对沙区生物结皮结构和生态功能影响的生物学机制提供了一定的理论依据。