Assessing the influence of physical,geochemical and biological factors on anaerobic microbial primary productivity within hydrothermal vent chimneys

Chemosynthetic primary production supports hydrothermal vent ecosystems, but the extent of that productivity and its governing factors have not been well constrained. To better understand anaerobic primary production within massive vent deposits, we conducted a series of incubations at 4, 25, 50 and 90 °C using aggregates recovered from hydrothermal vent structures. We documented in situ geochemistry, measured autochthonous organic carbon stable isotope ratios and assessed microbial community composition and functional gene abundances in three hydrothermal vent chimney structures from Middle Valley on the Juan de Fuca Ridge. Carbon fixation rates were greatest at lower temperatures and were comparable among chimneys. Stable isotope ratios of autochthonous organic carbon were consistent with the Calvin–Benson–Bassham cycle being the predominant mode of carbon fixation for all three chimneys. Chimneys exhibited marked differences in vent fluid geochemistry and microbial community composition, with structures being differentially dominated by gamma (γ) or epsilon (ε) proteobacteria. Similarly, qPCR analyses of functional genes representing different carbon fixation pathways showed striking differences in gene abundance among chimney structures. Carbon fixation rates showed no obvious correlation with observed in situ vent fluid geochemistry, community composition or functional gene abundance. Together, these data reveal that (i) net anaerobic carbon fixation rates among these chimneys are elevated at lower temperatures, (ii) clear differences in community composition and gene abundance exist among chimney structures, and (iii) tremendous spatial heterogeneity within these environments likely confounds efforts to relate the observed rates to in situ microbial and geochemical factors. We also posit that microbes typically thought to be mesophiles are likely active and growing at cooler temperatures, and that their activity at these temperatures comprises the majority of endolithic anaerobic primary production in hydrothermal vent chimneys.     

Microbial diversity of Loki's Castle black smokers at the Arctic Mid‐Ocean Ridge

Hydrothermal vent systems harbor rich microbial communities ranging from aerobic mesophiles to anaerobic hyperthermophiles. Among these, members of the archaeal domain are prevalent in microbial communities in the most extreme environments, partly because of their temperature‐resistant and robust membrane lipids. In this study, we use geochemical and molecular microbiological methods to investigate the microbial diversity in black smoker chimneys from the newly discovered Loki's Castle hydrothermal vent field on the Arctic Mid‐Ocean Ridge (AMOR) with vent fluid temperatures of 310–320 °C and pH of 5.5. Archaeal glycerol dialkyl glycerol tetraether lipids (GDGTs) and H‐shaped GDGTs with 0–4 cyclopentane moieties were dominant in all sulfide samples and are most likely derived from both (hyper)thermophilic Euryarchaeota and Crenarchaeota. Crenarchaeol has been detected in low abundances in samples derived from the chimney exterior indicating the presence of Thaumarchaeota at lower ambient temperatures. Aquificales and members of the Epsilonproteobacteria were the dominant bacterial groups detected. Our observations based on the analysis of 16S rRNA genes and biomarker lipid analysis provide insight into microbial communities thriving within the porous sulfide structures of active and inactive deep‐sea hydrothermal vents. Microbial cycling of sulfur, hydrogen, and methane by archaea in the chimney interior and bacteria in the chimney exterior may be the prevailing biogeochemical processes in this system.     

Effect of must characteristics on the diversity of Saccharomyces strains and their prevalence in spontaneous fermentations

Aims: The aim of this study was to investigate whether grapevine variety and must characteristics influence the diversity of Saccharomyces strains and their prevalence during spontaneous fermentations. Methods and results: Musts from different grapevine varieties, all of them autochthonous from Galicia, were used to perform spontaneous fermentations. Yeasts were isolated from the must and at the beginning, in the middle and at the end of fermentations. Those yeasts identified as Saccharomyces were characterized at the strain level by analysis of mtDNA‐RFLP. The results showed a low diversity of Saccharomyces strains, which was related to must sugar content and total acidity. Moreover, from a total of 44 different Saccharomyces strains, only eleven of them appeared at frequencies higher than 20% and were able to lead fermentations. A significant correlation between yeast strains and must acidity was observed, with the predominance of certain strains at high acidity values. Conclusions: Must characteristics, such as sugar content and acidity, influence the Saccharomyces strains diversity and the leader strains during fermentation. Significance and Impact of the Study: These results showed the adaptation of certain Saccharomyces strains to must with specific characteristics; this may be considered by winemakers for yeast inocula selection. Our findings have special relevance because this is the first study carried out in Galicia dealing with the influence of must properties on yeast strains that control fermentations.     

Parasitism,longevity and progeny production of six indigenous Kenyan trichogrammatid egg parasitoids (Hymenoptera: Trichogrammatidae) at different temperature and relative humidity regimes

Six native Kenyan species/strains of Trichogramma and Trichogrammatoidea, recovered from Helicoverpa armigera were evaluated at six different temperatures (10, 15, 20, 25, 30 and 35°C) and two relative humidity levels (40–50 and 70–80%) with the aim of selecting strains adapted to warmer temperature regimes. The species/strains were collected from low (<700 m), medium (between 700 and 1200 m) and high altitude (>1200 m) locations and were evaluated for parasitism, adult longevity, progeny production and progeny sex ratio at the different environmental regimes. Eggs of the factitious host, Corcyra cephalonica Stainton (Lepidoptera: Pyralidae) were used in the investigations. Temperature and humidity interactions affected parasitism and progeny production. The highest parasitism at the two humidity levels was at 25 and 30°C for all the strains evaluated. Adult longevity was also significantly affected by the interaction of temperature and relative humidity and was longer at the lower than higher relative humidity. Survival followed a type I survivorship curve at lower temperatures and a type III survivorship curve at the higher temperatures. Trichogramma sp. nr. mwanzai from low altitude, Trichogramma sp. nr. mwanzai from medium altitude and Trichogrammatoidea sp. nr. lutea also from medium altitude lived longer than other strains at all the temperatures and relative humidity levels evaluated, including the warmest regimes of 30 and 35°C. These strains appear promising as candidates for augmentative biocontrol of H. armigera in Kenya.     

Abundance and Diversity of Picocyanobacteria in Shallow Hydrothermal Vents of Panarea Island (Italy)

The abundance and diversity of cyanobacteria living in sediments collected from six vents (temperature range 37–130°C) close to the Panarea Island (Italy) were studied. The diversity of cyanobacteria was analyzed by using a PCR-DGGE approach with group-specific primers. The greatest number and diversity of cyanobacteria were registered at the coldest vent. Sequencing of DGGE fragments revealed that most sequences matched with uncultured cyanobacteria deposited in databases and some were distantly affiliated with different species of Synechococcus. New, genetically distant ribotypes of cyanobacteria are the dominant oxygenic phototrophs in shallow hydrothermal system of Panarea Island.     

Microbial Diversity at a Hot,Shallow-Sea Hydrothermal Vent in the Southern Tyrrhenian Sea (Italy)

Microbial community thriving at shallow hydrothermal vent named Black Point, close to the Island of Panarea in the Southern Tyrrhenian Sea (Italy), was studied by microscopic, cultural and molecular methods. New strains of Bacillus and Geobacillus were isolated. Members of sulphur-oxidizing bacteria, belonging to the genera Halothiobacillus and Thiomicrospira were demonstrated by both culture-dependent and -independent methods. Genetic diversity of Bacteria was higher than that of Archaea. Bacterial 16S rRNA gene sequences from Black Point showed low levels of similarity with other yet deposited sequences, suggesting that new bacterial phylotypes are present in this site. Dominant populations of Bacteria belonged to uncultured members of Proteobacteria (mainly of the class Gammaproteobacteria), Firmicutes and Acidobacteriaceae. Primary production appeared to be supported by chemosynthetic and photosynthetic bacteria affiliated with members of Gammaproteobacteria. Most of the archaeal sequences matched those of yet-uncultivated Archaea, thus their role at this vent is not well understood.     

SSU‐rRNA Gene Sequencing Survey of Benthic Microbial Eukaryotes from Guaymas Basin Hydrothermal Vent

Microbial eukaryotes have important roles in marine food webs, but their diversity and activities in hydrothermal vent ecosystems are poorly characterized. In this study, we analyzed microbial eukaryotic communities associated with bacterial (Beggiatoa) mats in the 2,000 m deep‐sea Guaymas Basin hydrothermal vent system using 18S rRNA gene high‐throughput sequencing of the V4 region. We detected 6,954 distinct Operational Taxonomic Units (OTUs) across various mat systems. Of the sequences that aligned with known protistan phylotypes, most were affiliated with alveolates (especially dinoflagellates and ciliates) and cercozoans. OTU richness and community structure differed among sediment habitats (e.g. different mat types and cold sediments away from mats). Additionally, full‐length 18S rRNA genes amplified and cloned from single cells revealed the identities of some of the most commonly encountered, active ciliates in this hydrothermal vent ecosystem. Observations and experiments were also conducted to demonstrate that ciliates were trophically active and ingesting fluorescent bacteria or Beggiatoa trichomes. Our work suggests that the active and diverse protistan community at the Guaymas Basin hydrothermal vent ecosystem likely consumes substantial amounts of bacterial biomass, and that the different habitats, often defined by distances of just a few 10s of cm, select for particular assemblages and levels of diversity.     

Intraspecific diversity in the fungal speciesChaunopycnis alba: Implications for microbial screening programs

Intraspecific variation among 84 isolates of the anamorphic fungusChaunopycnis alba from 26 different geographical locations was analyzed by investigating optimal growth temperatures, differences in the production of secondary metabolites and presence or absence of the cyclosporin synthetase gene. The genetic diversity was assessed using random amplified polymorphic DNA (RAPD). Analysis of these data showed high genetic, metabolic and physiological diversity within this species. Isolates from the Antarctic represented the most homogeneous group withinC. alba and together with isolates from the Arctic these polar strains differed from alpine, temperate and tropical strains by low optimal growth temperatures and by low production of secondary metabolites. Isolates from tropical climes were characterized by high optimal growth temperatures and by the production of comparatively diverse metabolite spectra. Most of the isolates that were similar in the combination of their physiological and metabolic characters were also genetically related. Isolates from different geographical origins did not show many similarities, with the exception of the cyclosporin A-producing isolates, and large diversity could be observed even within a single habitat. This leads us to the suggestion that for pharmaceutical screening programs samples should be collected from a diversity of different geographical and climatic locations. For the selection of strains for screening the RAPD assay seems to be the most powerful tool. It reflected the highest intraspecific diversity and the results corresponded well with the other characteristics.     

水稻种子内生泛菌(Pantoea spp.)系统发育多样性及其促生功能

【目的】Pantoea菌株是广泛分布在自然界中的一类功能多样的细菌。本研究对分离自水稻种子内生的Pantoea菌株进行系统发育分析及功能评价,从而确定分类地位、种类多样性、分布特征及功能特性。【方法】采用乙醇-次氯酸钠联合灭菌方法进行水稻种子的表面灭菌,进行内生细菌的分离与纯化;其次将纯化后的菌株进行16Sr RNA基因PCR扩增及序列分析,通过MEGA7软件构建系统发育树;将分离得到的菌株进行功能实验检测,如溶磷、产IAA、产铁载体、拮抗病原真菌等特性,最后检测菌株的溶血性;水稻分型采用SSR方法,并对水稻农学性状如分蘖数、株高、植株重及产量进行调查。【结果】本研究对分离自8个不同基因型水稻种子中的146株内生Pantoea菌株进行系统发育分析及功能评价,结果发现所分离到的泛菌菌株主要属于Pantoea dispersa、Pantoea agglomerans、Pantoea cypripedii以及Pantoea brenneri四个种,其中P. dispersa的菌株数量最多,分布最广,并且存在于所有的8个水稻种子样品中。对其中66株菌进行功能检测,发现86.3%和69.7%的菌株具有溶磷和产IAA能力,有7株菌具有产铁载体能力,未发现对真菌病害Fusarium moniliforme有拮抗作用的菌株,并发现3株菌具有溶血性;本实验未发现泛菌组成与水稻系统发育及农学性状存在明显的相关性。【结论】本研究首次对水稻种子中泛菌的多样性及其功能进行报道,发现不同基因型的水稻种子所含Pantoea种类及组成存在差异,种子选择性地积累了Pantoea类群,大部分菌株具有一定的促生特性。该研究结果有助于进一步探究微生物与植物的共进化、种子微生物的传播途径及作用方式。     

Temperature and strain effects on reproduction and survival of Trichogramma oleae and Trichogramma cacoeciae (Hymenoptera: Trichogrammatidae)

To assess differences in temperature sensitivity during development, life tables for two lines derived from the species Trichogramma oleae Voegelé and Pointel and a strain of Trichogramma cacoeciae Marchal (Hymenoptera: Trichogrammatidae) were elaborated at 15, 20, 25, 30, 35, 36, and 37°C in the laboratory. Eggs of Ephestia kuehniella Zeller together with a fresh drop of honey were supplied every 2 days until the death of the test females, and the removed host egg batches were placed in the equivalent rearing cabinet. The line ‘2F’ of T. oleae was found to be the most efficient at any range of temperatures except at 20 and 37°C, in comparison to the other tested strains. For all species, no progeny emerged from eggs incubated at 36°C and none of the parasitized eggs turned black at 37°C. The better performance at a broader range of temperatures by T. oleae (line 2 F) might be caused by a shorter history in artificial rearing in comparison to the other strains. Fewer generations at laboratory conditions and frequent multiplication on eggs of its natural host (the olive moth Prays oleae) may have prevented a deterioration in the rearing population of this strain, maintaining its genetic diversity at a higher scale. Applying varying temperature regimes on the rearing stock at regular intervals during the mass production process may help to maintain the essential quality of the biological control agents for field performance at higher temperatures.     

接种发酵和自然发酵中酿酒酵母菌株多样性比较

[目的]探究自然发酵和接种发酵两种发酵方式,对霞多丽葡萄发酵中酵母菌种多样性和酿酒酵母菌株遗传多样性的影响.[方法]以霞多丽葡萄为原料,分别进行自然发酵和接种不同酿酒酵母菌株(NXU 17-26、UCD522和UCD2610)的发酵,利用26S rDNA D1/D2区序列分析和Interdelta指纹图谱技术分别进行酵...     

南大西洋深海热液区可培养硫氧化微生物多样性及其硫氧化特性

【目的】探索南大西洋热液环境中的硫氧化细菌多样性并研究其硫氧化特性。【方法】通过富集培养和分离纯化获得硫氧化细菌,利用变性梯度凝胶电泳(DGGE)分析富集菌群组成结构,采用离子色谱法对获得的硫氧化细菌硫氧化特性进行检测。【结果】从南大西洋深海环境样品中共分离到48株菌,分属于alpha-Proteobacteria(28株,58.3%)、Actinobacteria(11株,22.9%)和gama-Proteobacteria(9株,18.8%)共3个门,其中Thalassospira、Martelella和Microbacterium为优势属。DGGE结果表明深海热液环境样品中微生物多样性丰富且不同站位存在差异。硫氧化特性研究结果表明,约60%的分离菌株具有硫氧化能力,可以氧化S_2O_3~(2–)生成SO_4~(2–)。获得一株硫氧化能力较强的潜在新种L6M1-5,在实验条件下可高效氧化S_2O_3~(2–),最大氧化速率可达0.56 mmol/(L·h)。【结论】南大西洋深海热液环境中可培养硫氧化细菌多样性丰富,为研究热液环境中的硫循环过程提供了实验材料和理论参考;同时高效硫氧化菌的获得,为工业化含硫废水的处理提供了良好的菌种资源。     

海南西海岸真红树内生放线菌多样性及其延缓衰老活性初筛

为了发掘红树林内生放线菌资源和进行新型海洋药物研究,该文选择海南西海岸14种真红树的根、茎、叶、花、胚轴为研究对象,采用9种不同分离培养基[改良的高氏培养基(AGG)、海藻糖-天冬酰胺培养基(M4)、海藻糖-脯氨酸培养基(M5)、改良ISP5培养基(M7)、精氨酸-天冬酰胺培养基(M9)、改良淀粉-水解酪素培养基(M10)、酪氨酸-天冬酰胺培养基(P7)、燕麦培养基(P3)、棉籽糖-组氨酸培养基(M11)],结合稀释涂布法和三线划线法从真红树组织中分离菌株,基于菌株16S rRNA基因序列信息等分子生物学鉴定方法对获得的海洋放线菌进行多样性分析,并使用模式生物秀丽隐杆线虫对所得内生放线菌的延缓衰老活性进行研究。结果表明:(1)从46份真红树组织中共获得24株放线菌,隶属于7科11属,其中9株菌株为链霉菌属(Streptomyces),且IMDGX 6270、IMDGX 6137和IMDGX 6173为3株疑似潜在新菌株。(2)秀丽隐杆线虫模型筛选发现4株放线菌(IMDGX 6157、IMDGX 6182、IMDGX 6248、IMDGX 6360)具有延缓衰老的活性,与空白组比较,生存时间分别延长17.16%、28.11%、29.05%、27.10%。综上结果说明海南西海岸区域真红树植物中可能含有较丰富的放线菌资源,能够为延缓衰老药物的研发提供新来源。     

Deep-sea hydrothermal vent Epsilonproteobacteria encode a conserved and widespread nitrate reduction pathway (Nap)

Despite the frequent isolation of nitrate-respiring Epsilonproteobacteria from deep-sea hydrothermal vents, the genes coding for the nitrate reduction pathway in these organisms have not been investigated in depth. In this study we have shown that the gene cluster coding for the periplasmic nitrate reductase complex (nap) is highly conserved in chemolithoautotrophic, nitrate-reducing Epsilonproteobacteria from deep-sea hydrothermal vents. Furthermore, we have shown that the napA gene is expressed in pure cultures of vent Epsilonproteobacteria and it is highly conserved in microbial communities collected from deep-sea vents characterized by different temperature and redox regimes. The diversity of nitrate-reducing Epsilonproteobacteria was found to be higher in moderate temperature, diffuse flow vents than in high temperature black smokers or in low temperatures, substrate-associated communities. As NapA has a high affinity for nitrate compared with the membrane-bound enzyme, its occurrence in vent Epsilonproteobacteria may represent an adaptation of these organisms to the low nitrate concentrations typically found in vent fluids. Taken together, our findings indicate that nitrate reduction is widespread in vent Epsilonproteobacteria and provide insight on alternative energy metabolism in vent microorganisms. The occurrence of the nap cluster in vent, commensal and pathogenic Epsilonproteobacteria suggests that the ability of these bacteria to respire nitrate is important in habitats as different as the deep-sea vents and the human body.     

红海榄内生细菌多样性及其抑制鱼类致病菌活性研究

红海榄为红树科红海属植物,广泛分布于热带海岸的红树林中,为真红树植物的典型代表。该研究以广西山口红树林国家级自然保护区红海榄为对象,应用稀释涂布法和三线法从红海榄各组织中分离出17株内生细菌,通过各菌株形态特征观察及利用16S rRNA序列基因和韦恩图分析其内生细菌多样性。结果表明:17株内生细菌分属3个门5科7属8种,Micromonospora和Mangrovibacter属为其优势类群。进一步分析发现红海榄根茎叶等组织的内生细菌类群差别较大,仅有1个相同菌属,17株菌中有3株菌与已有细菌物种典型菌株的全长16S rRNA基因相似性低于97%,代表着潜在的新属或新种。运用纸片法研究8株内生细菌发酵液的乙酸乙酯提取物对鱼类致病菌副溶血弧菌活性抑制效果,发现3株内生细菌(H003、H013、H009,浓度5 mg·m L-1)的代谢产物对副溶血弧菌具有较强的抑菌活性,其抑菌圈直径分别达到(8.4±0.07)、(8.2±0.07)、(8.3±0.14)mm。该研究结果表明红海榄中具有较好的内生细菌多样性和抑菌活性,为今后研究其内生细菌的化学多样性及其应用提供了重要的物质基础。     

Diversity of Meiofauna from the 9°50′N East Pacific Rise across a Gradient of Hydrothermal Fluid Emissions

Background

We studied the meiofauna community at deep-sea hydrothermal vents along a gradient of vent fluid emissions in the axial summit trought (AST) of the East Pacific Rise 9°50′N region. The gradient ranged from extreme high temperatures, high sulfide concentrations, and low pH at sulfide chimneys to ambient deep-sea water conditions on bare basalt. We explore meiofauna diversity and abundance, and discuss its possible underlying ecological and evolutionary processes.

Methodology/Principal Findings

After sampling in five physico-chemically different habitats, the meiofauna was sorted, counted and classified. Abundances were low at all sites. A total of 52 species were identified at vent habitats. The vent community was dominated by hard substrate generalists that also lived on bare basalt at ambient deep-sea temperature in the axial summit trough (AST generalists). Some vent species were restricted to a specific vent habitat (vent specialists), but others occurred over a wide range of physico-chemical conditions (vent generalists). Additionally, 35 species were only found on cold bare basalt (basalt specialists). At vent sites, species richness and diversity clearly increased with decreasing influence of vent fluid emissions from extreme flow sulfide chimney (no fauna), high flow pompei worm (S: 4–7, H''_loge: 0.11–0.45), vigorous flow tubeworm (S: 8–23; H''_loge: 0.44–2.00) to low flow mussel habitats (S: 28–31; H''_loge: 2.34–2.60).

Conclusions/Significance

Our data suggest that with increasing temperature and toxic hydrogen sulfide concentrations and increasing amplitude of variation of these factors, fewer species are able to cope with these extreme conditions. This results in less diverse communities in more extreme habitats. The finding of many species being present at sites with and without vent fluid emissions points to a non endemic deep-sea hydrothermal vent meiofaunal community. This is in contrast to a mostly endemic macrofauna but similar to what is known for meiofauna from shallow-water vents.     

八门湾红树林土壤小单孢菌的分离及其多样性

采用平板稀释法从海南八门湾红树林潮间带、木果榄和海莲红树根际土壤样品中分离和筛选小单孢菌科放线菌,对其分离方法进行了评价和比较,并通过16S rRNA基因测序探索了八门湾红树林小单孢菌科放线菌的多样性。采用4种预处理方法和5种分离培养基,经过排除重复菌株后共得到115株放线菌。16S rRNA基因测序结果显示,这些放线菌分布在5个科、9个属。其中小单孢菌科的菌株约占全部菌株的90%(105株),主要分布于3个属:Micromonospora(85%),Jishengella(9.5%)和Verrucosispora(5.5%),与其亲缘关系最近的菌株的相似性分布于98.5%~100%之间。     

Genetic Diversity： Geographical Distribution and Toxin Profiles of Microcystis Strains （Cyanobacteria） in China

Twenty strains of Microcystis Kütz were isolated from different freshwater bodies in China to analyze the diversity, geographical distribution and toxin profiles. Based on whole-cell polymerase chain reaction of cpcBA-IGS nucleotlde sequence, the derived neighbor-joining （NJ） and maximum parsimony （MP） trees Indicate that these strains of Microcystis can be divided into four clusters. The strains from south, middle and north region of China formed distinct lineages, suggesting high diversity and a geographical distribution from south to north locations. Moreover, the results being indicating high variable genotypes of the strains of the Microcystis strains from the same lake show that there Is high diversity of Microcystis within a water bloom population. Comparing the results of the present study with those reported for compared with 43 strains of Microcystis from other locations, also reveals Chinese strains have high similarity with those from regions in the North Hemispherical. This suggests that the Microcystis strains In the world might have a geographical distribution. Analysis of 30 strains using the primers MCF/TER and TOX2P/TOX2M showed that there was no correlation between the gene of cpcBA-IGS and the presence of racy. Toxic strains were founded to be predominant in different water bodies throughout China.     

Diversity of nitrogen-fixing cyanobacteria under various ecosystems of Thailand: I. Morphology,physiology and genetic diversity

The diversity among 853 isolates of nitrogen-fixing cyanobacteria obtained from soil samples collected from different ecosystems including mountainous, forest and cultivated areas in the central, northern and northeastern regions of Thailand was examined. Most isolates showed slow growth rate and had filamentous, heterocystous cells. The percentage of heterocysts in the filaments of different isolates varied from 8.3 to 9.6. Only a few strains showed high nitrogen-fixing potential, while most of the strains exhibited low capacity for nitrogen fixation. Anabaena and Nostoc were the dominant genera among these isolates. One hundred and two isolates were randomly selected from this diverse collection to determine the extent of genetic diversity on the basis of DNA fingerprinting using the PCR method. Based on the PCR products obtained by using a combination of three primers, all strains could be distinguished from one another. When a subset of 45 isolates of Nostoc and a subset of 44 isolates of Anabaena were further analysed by PCR, a wide range of diversity was observed within each of these genera.