New Undescribed Lineages of Non-extremophilic Archaea Form a Homogeneous and Dominant Element Within Alpine Moonmilk Microbiomes

The moonmilk deposits within the alpine Hundsalm cave in Austria offered the opportunity to investigate anthropogenically uninfluenced microbiomes. Via cultivation experiments we were able to show that the communities were cold-adapted and oligotrophic. Combined qPCR, DGGE, cloning and sequencing data further highlighted that the archaeal community basically comprises a low number of species, though highly abundant. These organisms are assumed to form new lineages within the Euryarchaeota, while the detected Thaumarchaeota, closely related to ammonium oxidizers, form a second, but minor, abundant group within the moonmilk deposits. Moreover, in terms of abundance the archaeal community clearly outnumbers bacteria (e.g., genera Pseudomonas, Flavobacterium and Rhodococcus) and fungi within the investigated microbiomes. In contrast to the highly complex bacterial and fungal communities, only a low number of archaeal species form a constant and essential element within the moonmilk speleothems and other cave-internal habitats.     

Changes in Prokaryote and Eukaryote Assemblages Along a Gradient of Hydrocarbon Contamination in Groundwater

Groundwater biota are particularly sensitive to environmental perturbations such as groundwater contamination. The diversity of prokaryotic and eukaryotic biota has been examined along a gradient of chlorinated hydrocarbon (CHC) contamination in the Botany Sands, an urban coastal sand-bed aquifer (Sydney, Australia). Molecular techniques were used to analyze the richness and composition of prokaryote and eukaryote assemblages using 16S and 18S rDNA, respectively. Taxon richness did not change significantly along the gradient for either prokaryotes or eukaryotes; however, significant shifts in assemblage composition were evident for both groups. Assemblage changes were most strongly correlated with concentrations of the major CHC, cis-1,2-dichloroethene, but the concentrations of a number of the contaminants were also correlated, making it difficult to infer if effects were due to any particular contaminant. The presence of cis-1,2-dichloroethene and other secondary ethenes suggests in situ breakdown of the primary CHCs via natural attenuation. The current focus of management of the Botany aquifer is to stop the contaminant plume reaching the adjoining estuary. This approach is clearly justified given the changes evident in the microbial assemblages in the groundwater, which are a likely consequence of the contamination.     

Phylogenetic Estimation of Community Composition and Novel Eukaryotic Lineages in Base Mine Lake: An Oil Sands Tailings Reclamation Site in Northern Alberta

Reclamation of anthropogenically impacted environments is a critical issue worldwide. In the oil sands extraction industry of Alberta, reclamation of mining‐impacted areas, especially areas affected by tailings waste, is an important aspect of the mining life cycle. A reclamation technique currently under study is water‐capping, where tailings are capped by water to create an end‐pit lake (EPL). Base Mine Lake (BML) is the first full‐scale end‐pit lake in the Alberta oil sands region. In this study, we sequenced eukaryotic 18S rRNA genes recovered from 92 samples of Base Mine Lake water in a comprehensive sampling programme covering the ice‐free period of 2015. The 565 operational taxonomic units (OTUs) generated revealed a dynamic and diverse community including abundant Microsporidia, Ciliata and Cercozoa, though 41% of OTUs were not classifiable below the phylum level by comparison to 18S rRNA databases. Phylogenetic analysis of five heterotrophic phyla (Cercozoa, Fungi, Ciliata, Amoebozoa and Excavata) revealed substantial novel diversity, with many clusters of OTUs that were more similar to each other than to any reference sequence. All of these groups are entirely or mostly heterotrophic, as a relatively small number of definitively photosynthetic clades were amplified from the BML samples.     

Molecular diversity analysis of rumen methanogenic Archaea from goat in eastern China by DGGE methods using different primer pairs

Aims:  To screen a pair of primers suitable for denaturing gradient gel electrophoretic (DGGE) analysis of ruminal methanogenic Archaea and to detect the archaeal communities in the rumen of goat.
Methods and Results:  Nine primer pairs for 16S rDNA of methanogenic Archaea , including six for directed polymerase chain reaction (PCR) and three for nested PCR were first evaluated by PCR amplification of the total DNA from rumen fluids and bacteria. The DGGE analysis of rumen fluids was then conducted with three primer sets (344fGC/915r, 1106fGC/1378r and 519f/915rGC) of the nine pairs tested. Good separation and quality of patterns were obtained in DGGE analysis with primer pairs 1106fGC/1378r and 519f/915rGC. A total of 40 DNA fragments were excised from the DGGE gels and their sequences were determined. All fragments belonged to methanogenic Archaea while primer pair 519f/915rGC had better amplification ranges than the other two primer pairs.
Conclusions:  The procedure of DGGE analysis with primer pair 519f/915rGC was more suitable for investigating methanogenic archaeal community in the rumen. The dominant methanogenic Archaea in the rumen of goat was Methanobrevibacter sp. and an unidentified methanogenic Archaea .
Significance and Impact of the Study:  One pair of primers suitable for DGGE analysis of ruminal methanogenic Archaea was obtained and the molecular diversity of ruminal methanogenic Archaea in goat was investigated by PCR-DGGE.     

Diversity of Archaea Communities within Contaminated Sand Samples from Johnston Atoll

A molecular 16S rRNA gene (SSU rDNA) analysis was performed for the determination of Archaea communities in polycyclic aromatic hydrocarbon (PAH)- and polychlorinated biphenyl (PCB)-contaminated sand samples obtained from Johnston Atoll. The objective of this study was to investigate Archaea community structure and phylogenetic diversity in a PAH- and PCB-contaminated marine environment that may potentially be intrinsically bioremediating these compounds. The clones obtained from this analysis were equally represented between the Crenarchaeota and Euryarchaeota phyla. This isolated marine environment is predominantly reef habitat, suggesting that the xenobiotic compounds introduced over time influenced the community structure of autochthonous Archaea. Phylogenetic diversity within these samples suggests that the resident Archaea populations were only distantly related to cultivated taxa and cloned sequences found in the public domain from both marine and terrestrial origins.     

Relating Microbial Community Structure and Geochemistry in Deep Regolith Developed on Volcaniclastic Rock in the Luquillo Mountains,Puerto Rico

Fe oxidation is often the first chemical reaction that initiates weathering and disaggregation of intact bedrock into regolith. Here we explore the use of pyrosequencing tools to test for evidence that bacteria participate in these reactions in deep regolith. We analyze regolith developed on volcaniclastic rocks of the Fajardo formation in a ridgetop within the rainforest of the Luquillo Mountains of Puerto Rico. In the 9-m-deep regolith profile, the primary minerals chlorite, feldspar, and pyroxene are detected near 8.3 m but weather to kaolinite and Fe oxides found at shallower depths. Over the regolith profile, both total and heterotrophic bacterial cell counts generally increase from the bedrock to the surface. Like other soil microbial studies, the dominant phyla detected are Proteobacteria, Acidobacteria, Planctomycetes, and Actinobacteria. Proteobacteria (α, β, γ and δ) were the most abundant at depth (6.8–9 m, 41–44%), while Acidobacteria were the most abundant at the surface (1.4–4.4 m, 37–43%). Despite the fact that Acidobacteria dominated surficial communities while Proteobacteria dominated near bedrock, the near-surface and near-bedrock communities were not statistically different in structure but were statistically different from mid-depth communities. Approximately 21% of all sequences analyzed did not match known sequences: the highest fraction of unmatched sequences was greatest at mid-depth (45% at 4.4 m). At the regolith-bedrock interface where weathering begins, several lines of evidence are consistent with biotic Fe oxidation. At that interface, iron-related bacterial activity tests and culturing indicate the presence of iron-related bacteria, and phylogenetic analyses identified sub-phyla containing known iron-oxidizing microorganisms. Cell densities of iron-oxidizers in the deep saprolite were estimated to be on the order of 10⁵ cells g^?1. Overall Fe loss was also observed at the regolith-bedrock interface, consistent with bacterial production of organic acids and leaching of Fe-organic complexes. Fe-organic species were also detected to be enriched near the bedrock-regolith interface. In this and other deep weathering profiles, chemolithoautotrophic bacteria that use Fe for energy and nitrate or oxygen as an electron acceptor may play an important role in initiating disaggregation of bedrock.     

Microbial Communities Promoting Mn(II) Oxidation in Ashumet Pond,a Historically Polluted Freshwater Pond Undergoing Remediation

An extensive culture-dependent and -independent study was conducted to identify microorganisms contributing to the biogeochemical cycling of manganese (Mn) in Ashumet Pond, a freshwater pond in Massachusetts currently undergoing remediation. A variety of bacteria (including Gamma-, Beta-, and Alpha-proteobacteria, Firmicutes, and Bacteroides) and Ascoymete fungi were isolated from the pond that promote Mn(II) oxidation and subsequent formation of Mn(III/IV) oxide minerals. Targeted-amplicon pyrosequencing of the bacterial and fungal communities associated with Mn oxide-encrusted samples show a highly diverse microbial community, of which the cultured phylotypes represent a minor proportion. This suggests a larger community, not identified through culturing, contributes to Mn oxide formation within the Pond.     

Using Stable Isotope Probing to Characterize Differences Between Free-Living and Sediment-Associated Microorganisms in the Subsurface

Aquifers are subterranean reservoirs of freshwater with heterotrophic bacterial communities attached to the sediments and free-living in the groundwater. In the present study, mesocosms were used to assess factors controlling the diversity and activity of the subsurface bacterial community. The assimilation of ¹³C, derived from ¹³C-acetate, was monitored to determine whether the sediment-associated and free-living bacterial community would respond similarly to the presence of protozoan grazers. We observed a dynamic response in the sediment-associated bacterial community and none in the free-living community. The disparity in these observations highlights the importance of the sediment-associated bacterial community in the subsurface carbon cycle.     

深海微生物多样性

海洋面积约占地球总面积的70％,平均深度3,800 m,海底平均压力38 MPa,海水以下更是包含有物理化学性质迥异的多种地质结构,例如海洋沉积物、洋壳、热液口以及冷泉等.这些性质迥异的地质结构环境造就了丰富的生物多样性,构成了地球上最大的微生物生态系统.深海海水中最主要的微生物类群是α-,γ-变形菌(Alpha-&Gammaproteobacteria),以及海洋古菌群I(Marine Group I).深海沉积物中微生物含量与有机物含量和距离大陆板块的距离相关,以异养微生物为主.深海冷泉区富集了厌氧甲烷氧化古菌ANME和硫酸盐还原菌(Deltaproteobacteria);深海热液区由于具有化学物质的多样性和快速的动态变化而导致形成微生物的高度多样性.洋壳主要由基性、超基性岩构成,含有丰富的矿物,其中不乏参与铁、锰、硫等关键代谢反应的化能自养微生物.同时,由于环境中99％以上的微生物没有已培养的亲缘种,因此对深海微生物的多样性、生理功能特性以及生物地球化学作用的理解和研究仍然存在巨大的挑战.本文将尝试从不同的深海环境分区来综述深海海水、沉积物、洋壳,以及冷泉区和热液口等特殊生态环境中微生物的分布和多样性.     

Predominance of Methanolobus spp. and Methanoculleus spp. in the Archaeal Communities of Saline Gas Field Formation Fluids

The microbial communities in sulfate-rich, saline formation fluids of a natural gas reservoir in Lower Saxony, Germany were investigated to enhance the knowledge about microbial communities in potential carbon dioxide sequestration sites. This investigation of the initial state of the deep subsurface microbiota is necessary to predict their influence on the long-term stability and storage capacity of such sites. While the bacterial 16S rDNA gene library was comprised of sequences affiliating with the Firmicutes, the Alphaproteobacteria, the Gammaproteobacteria and the Thermotogales, the archaeal 16S rDNA libraries were simply dominated by two phylotypes related to the genera Methanolobus and Methanoculleus. The monitoring of the archaeal communities in different formation fluid samples by T-RFLP and Real-Time-PCR indicated that these two methanogenic genera dominated at all, whereas the proportion of the two groups varied. Thus, methylotrophic and autotrophic methanogenesis seems to be of importance in the reservoir fluids, dependent on the provided reduction equivalents and substrates and it also may influence the fate of CO₂ in the subsurface.     

The Variation of Microbial Communities in a Depth Profile of Peat in the Gahai Lake Wetland Natural Conservation Area

The Gahai Lake wetland natural conservation area in northwestern China includes peatland that has been accumulating over hundreds of years and is seldom disturbed by industry. Bacteria and archaea in peat soil, which is a reservoir for carbon and water, may influence its ecological function. The objective of this study was to obtain a clearer understanding of peat microbial ecology and its relationship to the environmental conditions of this area. Hence, the microbial community of the peatland ecosystem was investigated by sequencing bacterial and archaeal DNA extracted from samples collected at different peat depths. Results showed that in all samples the dominant bacterial phyla were Proteobacteria (relative abundance 0.39 ± 0.12) and Chloroflexi (0.16 ± 0.09), while the dominant archaeal phyla were Miscellaneous Crenarchaeotic Group (MCG) (0.62 ± 0.21) and Euryarchaeota (0.27 ± 0.16). The diversity and microbial community structure at deeper depths (90 and 120 cm below the peat surface) significantly differ from that at shallower depths (10, 30 and 50 cm deep). In contrast to the shallow layers, the deeper layers became more abundant in the bacterial phyla Chloroflexi, Bacteroidetes, Atribacteria, Aminicenantes, Chlorobi, TA06, Caldiserica and Spirochaetae; and in the archaeal phyla MCG and Miscellaneous Euryarchaeotic Group (MEG). This study revealed a significant shift in microbial community in peat between 50 cm and 90 cm deep, as probably influenced by the oxygen supply at different depths. Furthermore, new insights into the microbial taxa were obtained, thus providing a baseline for future studies of this peat ecosystem.     

南亚热带森林优势种群荷木和锥栗在演替系列群落中的分子生态研究(英文)

用扩增片段长度多态性 (AFLP ,amplifiedfragmentlengthpolymorphism)方法研究了荷木 (SchimasuperbaGardn .etChamp .)和锥栗 (CastanopsischinensisHance .)在 3个演替系列群落中的分子变化。研究地点位于广东省鼎湖山。 3个群落是针叶林群落、针阔叶混交林群落和常绿阔叶林群落。荷木的AFLP分析结果表明 ,4组引物对分别扩增出2 4、40、2 7、2 7条带 ,其中分别有 15、2 3、2 3、16条是多样性带 ;锥栗的AFLP分析结果表明同样的 4组引物对分别扩增出 2 7、2 0、33、39条带 ,其中分别有 12、5、15、13条是多样性带。平均杂合度表明荷木比锥栗有更大的分子变异。用AMOVA(analysisofmolecularvariance)分析表明荷木种群有 95 .99%的分子分化表现在种群内 ,4.0 1%的分子分化表现在种群间 ,表现极显著 (P <0 .0 0 1) ;锥栗种群有 75 .36 %的分子分化表现在种群内 ,2 4.6 4%的分子分化表现在种群间 ,极显著 (P <0 .0 0 1)。除趋势面对应分析表明荷木来自不同群落的个体分布没有规律 ,而锥栗来自不同群落的个体大致分布在一起。上述结果的产生是两个不同种群的生物学特性的反映 ,并提示了不同群落微环境对种群分化的影响 ,以及与森林演替群落的相关性。     

南亚热带森林优势种群荷木和锥栗在演替系列群落中的分子生态研究

Amplified fragment length polymorphism（AFLP）was used to analyze 2 populations: Schima superba Gardn. et Ｃhamp. and Castanopsis chinensis Hance. across three different communities representing three succession stages, in Dinghu Mountain, China. These two were middle succession species in the lower subtropical broad-leaved forest. Four AFLP primer combinations using total 48 individuals of S. superba provided 24, 40, 27 and 27 reliable bands, of which 15, 23, 23 and 16 were polymorphic, respectively. Similarly, total 48 individuals of C. chinensis provided 27, 20, 33 and 39 reliable bands, of which 12, 5, 15 and 13 were polymorphic respectively. These bands were used as presence/absence data to assess the levels of genetic variation and population structure of those species. From average heterozygosity, S．superba possessed higher molecular variation than C．chinensis. Analysis of molecular variance（AMOVA）indicated that most of the genetic variation of S．superba was due to the differences within population（95.99%, P<0.001）, with 4.01%（P<0.001）genetic variation among population. Similarly, AMOVA indicated the most of the genetic variation of C. chinensis was due to the differences within population（75.36%, P<0.001）, with 24.64%（P<0.001）genetic variation among communities（24.64%）. DCA（Detrended Correspondence Analysis） analysis showed that the individuals of S．superba from the same community did not cluster together, while the individuals of C．chinensis from the same community roughly cluster together. The above results reflected the biological characteristics of the two different species suggesting the significant effect of microenvironment of different community on population differentiation and its relationship of which to forest succession resulted in genetic divergence.     

Soil-inhabiting Tardigrade Communities in Forests of Central Japan

This study was carried out for the purpose of detecting the relationship between soil-inhabiting tardigrade communities and environmental factors of various forests. Nine forests in the southern part of Kanagawa Prefecture, Central Japan, were selected for this study. Four vegetation types were designated; broadleaved (evergreen/deciduous), coniferous and orchard. In these sites, dry weight of leaf litter, soil pH, soil hardness, soil moisture content and porosity ratio were measured. Wet soil faunal frequencies were also described. The Baermann funnel method was adopted for collecting tardigrades, and DIC microscopy was used for specific identification. To clarify the correlation between environmental variables and tardigrade faunae, multivariate analysis was applied. The tardigrade fauna occurred as two distinct groups. The first group primarily contained Macrobiotus species. The second group contained the genus Diphascon (e.g. D. nobilei, D. patanei, D. prorsirostre). An exception to this was D. pingue, included in the former. Most of the Diphascon species were concentrated in Nebu (coniferous forest site), while, Macrobiotus species were dominant in other sites. Distinct environmental factors could not be identified, but the nematodal frequency was recognized as the main factor in forming these groups. The uniqueness of Nebu, which does not correspond to large-scaled vegetational classification, was substantiated by statistical data. Nebu’s coniferous forest apparently has created a unique environment for sustaining rare species (Diphascon species). This study concluded that forests should be evaluated not only by the macroscopic factors, such as landscape, but also by the microscopic communities, such as those including the tardigrades.     

Vertical and Horizontal Distribution of Bacterial Communities in Alluvial Groundwater of the Nakdong River Bank

As a collaborative effort to characterize a pilot test site for managed aquifer recharge (MAR), vertical and horizontal distributions of microbial communities in the river bank subsurface were investigated to assess the ecological effects after the operation of the MAR using the river water adjacent to the site. Along with a geochemical analysis, barcoded pyrosequencing was performed using the genomic DNAs extracted from the subsurface groundwater/sediment samples retrieved from three multilevel wells among the installed cluster of 14 boreholes. A total of 9 samples from 3 depths (10, 15–25, and 33 m below the ground surface) of each borehole showed higher bacterial abundance and diversity in the shallow (10 m) depths than in the deep (33 m) groundwater. In addition, there was a slight separation of the microbial communities between the depths based on the nonmetric multidimensional scaling analysis of the Yue and Clayton distance and the distance-weighted UniFrac analysis. The phylum Proteobacteria was dominant in all the samples at the sequence abundance of 64.0–97.8% with the total operational taxonomic units of 3375 at the species level, while among the total 288 genera, the genus Pseudomonas and an unclassified genus from Betaproteobacteria were the most abundant across the samples. The community separation between the shallow and the deep groundwater seemed to be correlated with depth differences, supported by differences in the dissolved oxygen (DO) concentration and oxidation-reduction potential (ORP). In the study site, unusually high values of electrical conductivity (EC) were found in the deep groundwater, but those values were unlikely to contribute to the community separation between the shallow and deep groundwater, unlike the DO and ORP values, which were found to influence the community differences.     

Methane Biogeochemistry and Methanogen Communities in Two Northern Peatland Ecosystems,New York State

Rates of methane (CH₄) production vary considerably among northern peat-forming wetlands, and it is not clear whether variability is caused by environmental factors affecting CH₄ production or differences in methanogen communities. We investigated CH₄ production and emission dynamics concomitantly with 16S rRNA gene sequence-based community analysis of Archaea in two contrasting peat-forming northern wetlands, an ombrotrophic bog and a minerotrophic conifer swamp. Individual measurements of CH₄ emissions to the atmosphere followed a lognormal distribution pattern in both sites, and mean rates were 30× greater in the bog site. Rates of CH₄ production measured in vitro were initially 3× greater in the bog than in the conifer swamp; although, after 30 days of incubation, production rates were similar suggesting that in situ environmental conditions limited production in the conifer swamp. Amplified ribosomal DNA restriction analysis (ARDRA) and rarefaction techniques indicated that both sites had similar levels of archaeal richness, with 27 unique taxa in the bog and 23 taxa in the conifer swamp. However, the bog had more pronounced dominance of a few taxa, whereas the conifer swamp had more even distribution among taxa. A 16S rRNA gene sequence-based phylogenetic analysis indicated high levels of diversity with similarity to known methanogenic families Methanosarcinaceae, Methanosaetaceae, Methanobacteriaceae, and likely Methanomicrobiaceae as well as two additional lineages previously characterized as groups of yet uncultivated Euryarchaeota commonly occurring in flooded rice soils. Therefore, sites with low and high rates of CH₄ production supported very diverse methanogenic communities.     

拉鲁湿地主要植物群落结构及物种多样性

2002年6~9月对拉鲁湿地植物种类、群落结构、生物量以及物种多样性进行了调查研究.结果表明:(1)拉鲁湿地共有植物30科52属85种,主要有芦苇[Phragmites australis(Cav.)Trin.ex Steud.](A)、尼伯尔酸模(RumexnepalensisSpreng)(B)、水葱(Scirpus validusVahl)(C)、穗状狐尾藻(MyriophyllumspicatumL.)(D)、灯芯草(Juncus effususL.)(E)、针叶苔草(CarexonoeiFranch.et Sav.)和黑褐苔草(CarexatrofuscaSchkuhr)(F)、藏北嵩草(KobresialittledaleiC.B.Clarke)(G)、藏蓟[Cirsiumlanatum(Roxb.ex Willd.)Spreng.](H)等8个主要植物群落.(2)在8个主要植物群落中,嵩草群落所含物种数最多,为44种,穗状狐尾藻群落最少,仅8种;芦苇群落生物量最高,为124.5~1 027.0 g/m2,藏蓟群落生物量最低,为124.5~220.5 g/m2;优势种芦苇的生物量最高,为183.5~660.0 g/m2,藏蓟生物量最低,为43.1~76.3 g/m2.(3)各群落的垂直结构特点是:芦苇群落、水葱群落、穗状狐尾藻群落具有挺水层、浮叶层和沉水层,其他群落只具有可分为高、低两层的草本层.(4)在各群落的相似性方面,嵩草群落与藏蓟群落、水葱群落与芦苇群落和尼伯尔酸模群落的相似性要明显高于其他群落,其Jaccard系数分别为0.549 0、0.538 5、0.500 0;芦苇群落、尼伯尔酸模群落、水葱群落、穗状狐尾藻群落与藏蓟群落以及芦苇群落、穗状狐尾藻群落与嵩草群落在建群种上没有相似之处,Jaccard系数为0.