Unique Microbial Community in Drilling Fluids from Chinese Continental Scientific Drilling

Circulating drilling fluid is often regarded as a contamination source in investigations of subsurface microbiology. However, it also provides an opportunity to sample geological fluids at depth and to study contained microbial communities. During our study of deep subsurface microbiology of the Chinese Continental Scientific Deep drilling project, we collected 6 drilling fluid samples from a borehole from 2290 to 3350 m below the land surface. Microbial communities in these samples were characterized with cultivation-dependent and -independent techniques. Characterization of 16S rRNA genes indicated that the bacterial clone sequences related to Firmicutes became progressively dominant with increasing depth. Most sequences were related to anaerobic, thermophilic, halophilic or alkaliphilic bacteria. These habitats were consistent with the measured geochemical characteristics of the drilling fluids that have incorporated geological fluids and partly reflected the in-situ conditions. Several clone types were closely related to Thermoanaerobacter ethanolicus, Caldicellulosiruptor lactoaceticus, and Anaerobranca gottschalkii, an anaerobic metal-reducer, an extreme thermophile, and an anaerobic chemoorganotroph, respectively, with an optimal growth temperature of 50–68°C. Seven anaerobic, thermophilic Fe(III)-reducing bacterial isolates were obtained and they were capable of reducing iron oxide and clay minerals to produce siderite, vivianite, and illite. The archaeal diversity was low. Most archaeal sequences were not related to any known cultivated species, but rather to environmental clone sequences recovered from subsurface environments. We infer that the detected microbes were derived from geological fluids at depth and their growth habitats reflected the deep subsurface conditions. These findings have important implications for microbial survival and their ecological functions in the deep subsurface.     

Geomicrobiology of deep-sea deposits: estimating community diversity from low-temperature seafloor rocks and minerals

The role of deep‐sea microbial communities in the weathering of hydrothermal vent deposits is assessed using mineralogical and molecular biological techniques. The phylogenetic diversity of varied deep‐sea bare rock habitats associated with the oceanic spreading centre at the Juan de Fuca Ridge was accessed using restriction fragment length polymorphism (RFLP) and rDNA sequencing. The mineralogical composition of the deposits used for phylogenetic analysis was determined by X‐ray diffraction in order to determine the proportion and composition of sulphide minerals, and to determine degree of alteration associated with each sample. RFLP analyses resulted in 15 unique patterns, or Operational Taxonomic Units (OTUs). Most environments examined were dominated by only one or two OTUs, which often comprised approximately 60% of the rDNA clones generated from that environment. Only one environment, the Mound, had a representative rDNA clone from every OTU identified in this study. For one other environment, ODP sediments, rDNA clones were all contained in a single OTU. The diversity of the microbial community is found to decrease with decreasing reactivity of the sulphide component in the samples and with increasing presence of alteration products. Phylogenetic analyses reveal that OTUs contain representatives of the epsilon‐, beta‐ and gamma‐subdivisions of the Proteobacteria. OTU1, which dominates clone libraries from every environment and is increasingly dominant with increasing rock alteration, is closely related to a group of chemolithoautotrophic iron‐oxidizing bacteria that have been recently isolated from the deep sea. The apparent abundance and widespread distribution within the samples examined of the putative iron‐oxidizing bacteria that may be represented by OTU1 suggests that this physiological group could play an important role in rock‐weathering and carbon fixation at the seafloor.     

The trade-off between growth rate and yield in microbial communities and the consequences for under-snow soil respiration in a high elevation coniferous forest

Soil microbial respiration is a critical component of the global carbon cycle, but it is uncertain how properties of microbes affect this process. Previous studies have noted a thermodynamic trade-off between the rate and efficiency of growth in heterotrophic organisms. Growth rate and yield determine the biomass-specific respiration rate of growing microbial populations, but these traits have not previously been used to scale from microbial communities to ecosystems. Here we report seasonal variation in microbial growth kinetics and temperature responses (Q₁₀) in a coniferous forest soil, relate these properties to cultured and uncultured soil microbes, and model the effects of shifting growth kinetics on soil heterotrophic respiration (R_h). Soil microbial communities from under-snow had higher growth rates and lower growth yields than the summer and fall communities from exposed soils, causing higher biomass-specific respiration rates. Growth rate and yield were strongly negatively correlated. Based on experiments using specific growth inhibitors, bacteria had higher growth rates and lower yields than fungi, overall, suggesting a more important role for bacteria in determining R_h. The dominant bacteria from laboratory-incubated soil differed seasonally: faster-growing, cold-adapted Janthinobacterium species dominated in winter and slower-growing, mesophilic Burkholderia and Variovorax species dominated in summer. Modeled R_h was sensitive to microbial kinetics and Q₁₀: a sixfold lower annual R_h resulted from using kinetic parameters from summer versus winter communities. Under the most realistic scenario using seasonally changing communities, the model estimated R_h at 22.67 mol m⁻² year⁻¹, or 47.0% of annual total ecosystem respiration (R_e) for this forest.     

柴达木盆地尕斯库勒盐湖区邻近水体对湖泊微生物群落的贡献

【目的】探究尕斯库勒盐湖生态系统中邻近水体对湖泊微生物的贡献。【方法】采集尕斯库勒盐湖区湖水、沉积物以及邻近的泉水、河水和盐田的水样,对其进行地球化学分析;通过16S rRNA基因的Illumina MiSeq高通量测序分析样品的微生物群落组成。【结果】尕斯库勒盐湖区水体和沉积物中的优势门是变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)、放线菌门(Actinobacteria)和广古菌门(Euryarchaeota)。盐度和pH是影响尕斯库勒盐湖区群落组成的最主要环境因素。邻近水体对湖泊水体和沉积物的贡献分别为12.94%和7.53%。【结论】邻近水体对尕斯库勒盐湖微生物群落的贡献有限。     

Organic sulfur metabolisms in hydrothermal environments

Sulfur is central to the metabolisms of many organisms that inhabit extreme environments. While biotic and abiotic cycling of organic sulfur compounds has been well documented in low‐temperature anaerobic environments, cycling of organic sulfur in hydrothermal environments has received less attention. Recently published thermodynamic data have been used to estimate aqueous alkyl thiol and sulfide activities in deep‐sea hydrothermal systems. Here we use geochemical mixing models to predict fluid compositions that result from mixing end‐member hydrothermal fluid from the East Pacific Rise with bottom seawater. These fluid compositions are combined with estimates of methanethiol and dimethylsulfide activities to evaluate energy yields for potential organic sulfur‐based metabolisms under hydrothermal conditions. Aerobic respiration has the highest energy yields (over ?240 kJ/mol e^?) at lower temperature; however, oxygen is unlikely to persist at high temperatures, restricting aerobic respiration to mesophilic communities. Nitrite reduction to N₂ has the highest energy yields at higher temperatures (greater than ～40 °C). Nitrate and nitrite reduction to ammonium also yield significant energy (up to ?70 kJ/mol e^?). Much lower, but still feasible energy yields are calculated for sulfate reduction, disproportionation, and reduction with H₂. Organic compound family and the activity of methanethiol and dimethylsulfide were less important than metabolic strategy in determining overall energy yields. All metabolic strategies considered were exergonic within some portion of the mixing regime suggesting that organic sulfur‐based metabolisms may be prevalent within deep‐sea hydrothermal vent microbial communities.     

地质封存二氧化碳与深地微生物相互作用研究进展

地质封存将工业和能源相关领域生产活动产生的二氧化碳（CO₂）进行捕集并注入到深部地下岩石构造中,以实现长期储存的目标,是降低温室气体排放、实现CO₂长期封存的重要可行性手段之一。向深部地下地质构造中注入大量CO₂会导致深地环境发生显著变化,进而引起原生微生物活性及群落结构发生明显改变。因此,地质封存CO₂能够直接或间接影响深地微生物驱动的生物地球化学过程。同时,微生物在短期和长期的超临界CO₂（scCO₂）胁迫作用下,也会通过不同的适应性进化方式影响CO₂在地下环境中的迁移、转化和赋存形态。本文介绍了国内外二氧化碳捕获与封存发展现状以及地质封存CO₂影响条件下的scCO₂-水-微生物-矿物的相互作用领域的最新科研进展,并展望了利用深地微生物强化CO₂固定以及将其转化为高附加值产物的潜力。     

硫酸盐对淡水养殖池塘表层底泥微生物的影响

硫酸盐引起的生态学效应已得到了越来越多的关注,但目前关于硫酸盐对养殖池塘底泥微生物的影响还知之甚少。【目的】探究不同浓度硫酸盐对养殖池塘底泥微生物的影响规律及可能的机制。【方法】本研究利用采集自养殖池塘的底泥和表层水构建了试验系统,研究了加入约0 mg/L （对照组）、30 mg/L （T1处理组）、150 mg/L （T2处理组）、500 mg/L （T3处理组） Na₂SO₄后表层底泥微生物的丰度、多样性、组成和共生网络的变化规律,并分析了环境影响因素。【结果】孵育第30天前,各实验组底泥微生物变化不大;但到第50天时,T2和T3处理组微生物丰度和多样性相比对照组均明显下降。相比其他实验组,T1处理组酸杆菌门（Acidobacteriota）、拟杆菌门（Bacteroidota）相对丰度出现显著升高（P<0.05）,T3处理组变形菌门（Proteobacteria）和放线菌门（Actinobacteriota）相对丰度出现显著升高（P<0.05）。与对照组相比,T1处理组增加了较多差异类群（62种）,而T3处理组差异类群大量减少（45种）。共生网络图分析显示硫酸盐浓度的增加引起了底泥微生物网络复杂性的增加,说明微生物群落可能通过自身的调节来响应硫酸盐引起的环境改变。冗余分析（redundant analysis,RDA）和相关性分析揭示底泥总有机碳、总氮和氧化还原电位是影响底泥微生物的主要环境因素,提示底泥微生物可能受到硫酸盐和有机质作用的影响。【结论】较长时间的高浓度硫酸盐会对池塘底泥微生物群落造成重要影响,微生物群落自身的转变和硫酸盐引起的有机质分解改变可能是造成微生物群落变化的关键因素。     

Environmental switching during biofilm development in a cold seep system and functional determinants of species sorting

The functional basis for species sorting theory remains elusive, especially for microbial community assembly in deep‐sea environments. Using artificial surface‐based biofilm models, our recent work revealed taxonomic succession during biofilm development in a newly defined cold seep system, the Thuwal cold seeps II, which comprises a brine pool and the adjacent normal bottom water (NBW) to form a metacommunity via the potential immigration of organisms from one patch to another. Here, we designed an experiment to investigate the effects of environmental switching between the brine pool and the NBW on biofilm assembly, which could reflect environmental filtering effects during bacterial immigration to new environments. Analyses of 16S rRNA genes of 71 biofilm samples suggested that the microbial composition of biofilms established in new environments was determined by both the source community and the incubation conditions. Moreover, a comparison of 18 metagenomes provided evidence for biofilm community assembly that was based primarily on functional features rather than taxonomic identities; metal ion resistance and amino acid metabolism were the major species sorting determinants for the succession of biofilm communities. Genome binning and pathway reconstruction of two bacterial species (Marinobacter sp. and Oleispira sp.) further demonstrated metal ion resistance and amino acid metabolism as functional traits conferring the survival of habitat generalists in both the brine pool and NBW. The results of this study shed new light on microbial community assembly in special habitats and bridge a gap in species sorting theory.     

The Origin and Age of Biogeochemical Trends in Deep Fracture Water of the Witwatersrand Basin,South Africa

Water residing within crustal fractures encountered during mining at depths greater than 500 meters in the Witwatersrand basin of South Africa represents a mixture of paleo-meteoric water and 2.0–2.3 Ga hydrothermal fluid. The hydrothermal fluid is highly saline, contains abiogenic CH ₄ and hydrocarbon, occasionally N ₂ , originally formed at ～ 250–300°C and during cooling isotopically exchanged O and H with minerals and accrued H ₂ , ⁴ He and other radiogenic gases. The paleo-meteoric water ranges in age from ～ 10 Ka to > 1.5 Ma, is of low salinity, falls along the global meteoric water line (GMWL) and is CO ₂ and atmospheric noble gas-rich. The hydrothermal fluid, which should be completely sterile, has probably been mixing with paleo-meteoric water for at least the past ～100 Myr, a process which inoculates previously sterile environments at depths > 2.0 to 2.5 km. Free energy flux calculations suggest that sulfate reduction is the dominant electron acceptor microbial process for the high salinity fracture water and that it is 10 ⁷ times that normally required for cell maintenance in lab cultures. Flux calculations also indicate that the potential bioavailable chemical energy increases with salinity, but because the fluence of bioavailable C, N and P also increase with salinity, the environment remains energy-limited. The ⁴ He concentrations and theoretical calculations indicate that the H ₂ that is sustaining the subsurface microbial communities (e.g. H ₂ -utilizing SRB and methanogens) is produced by water radiolysis at a rate of ～1 nM yr ^?1 . Microbial CH ₄ mixes with abiogenic CH ₄ to produce the observed isotopic signatures and indicates that the rate of methanogenesis diminishes with depth from ～ 100 at < 1 kmbls, to < 0.01 nM yr ^?1 at > 3 kmbls. Microbial Fe(III) reduction is limited due to the elevated pH. The δ¹³C of dissolved inorganic carbon is consistent with heterotrophy rather than autotrophy dominating the deeper, more saline environments. One potential source of the organic carbon may be microfilms present on the mineral surfaces.     

The role of environmental factors for the composition of microbial communities of saline lakes in the Novosibirsk region (Russia)

Background

Nothing is currently known about microbial composition of saline lakes of the Novosibirsk region and its dependence on physical-chemical parameters of waters. We studied the structure of microbial communities of saline lakes of the Novosibirsk region and the effect of physical-chemical parameters of waters on microbial communities of these lakes.

Results

According to the ion content, the lakes were classified either as chloride or chloride-sulfate types. Water salinity ranges from 4.3 to 290 g L⁻¹. Many diverse microbial communities were found. Filamentous and colonial Cyanobacteria of the genera Scytonema, Aphanocapsa, and/or filamentous Algae dominated in littoral communities. Spatial and temporal organization of planktonic microbial communities and the quantities of Archaea and Bacteria were investigated using fluorescent in situ hybridization. We have found that the dominant planktonic component is represented by Archaea, or, less frequently, by Bacteria. Various phylogenetic groups (Bacteria, Archaea, Algae, and Cyanobacteria) are nonuniformly distributed. The principal component analysis was used to detect environmental factors that affect microorganism abundance. We found the principal components responsible for 71.1 % of the observed variation. It was demonstrated that two-block partial least squares was a better method than principal component analysis for analysis of the data. We observed general relationships between microbial abundance and water salinity.

Conclusions

We have performed the first-ever study of the structure of the microbial communities of eleven saline lakes in the Novosibirsk region along with their physical-chemical parameters of waters. Our study demonstrates that saline lakes in the Novosibirsk region contain a unique microbial communities that may become a prolific source of microorganisms for fundamental and applied studies in various fields of ecology, microbiology, geochemistry, and biotechnology, and deserve further metagenomic investigation.

     

Dissolved Organic Matter Concentration and Quality Influences upon Structure and Function of Freshwater Microbial Communities

Past studies have suggested that the concentration and quality of dissolved organic matter (DOM) may influence microbial community structure. In this study, we cross-inoculated the bacterial communities from two streams and a dystrophic lake that varied in DOM concentration and chemistry, to yield nine fully crossed treatments. We measured dissolved organic carbon (DOC) concentration and heterotrophic microbial community productivity throughout a 72-h incubation period, characterized DOM quality by molecular weight, and determined microbial community structure at the initial and final time points. Our results indicate that all bacterial inoculate sources had similar effects upon DOC concentration and DOM quality, regardless of the DOM source. These effects included an overall decrease in DOM M _W and an initial period of DOC concentration variability between 0-24h. In contrast, microbial communities and their metabolic rates converged to profiles that reflected the DOM source upon which they were growing, regardless of the initial bacterial inoculation. The one exception was that the bacterial community from the low-concentration and low-molecular-weight DOM source exhibited a greater denaturing gradient gel electrophoresis (DGGE) band richness when grown in its own DOM source than when grown in the highest concentration and molecular weight DOM source. This treatment also exhibited a higher rate of productivity. In general, our data suggest that microbial communities are selected by the DOM sources to which they are exposed. A microbial community will utilize the low-molecular-weight (or labile) DOM sources as well as parts of the high-molecular-weight (refractory) DOM, until a community develops that can efficiently metabolize the more abundant high-molecular-weight source. This experiment examines some of the complex interactions between microbial community selection and the combined factors of DOM quality and concentration. Our data suggest that the roles of aerobic aquatic heterotrophic bacteria in carbon cycling, as well as the importance of high-molecular-weight DOM as a carbon source, may be more complex than is conventionally recognized.     

青藏高原三个盐碱湖的产甲烷菌群和产甲烷代谢途径分析

【目的】分析青藏高原不同类型盐碱湖中的优势产甲烷菌群和优势产甲烷代谢途径。【方法】以不同盐度和植被类型的公珠错、昆仲错和无植被的兹格塘错的沉积物为研究对象,通过高通量测序和q PCR定量古菌16S r RNA多样性分析优势古菌类群;模拟原位盐浓度及p H,比较不同产甲烷底物(甲醇、三甲胺、乙酸和H_2/CO_2)富集沉积物的产甲烷速率,分析其优势产甲烷菌代谢类型。通过添加产甲烷抑制剂(2-溴乙烷磺酸盐),检测沉积物中产甲烷底物积累,确定不同盐碱湖中主要的产甲烷途径。【结果】昆仲错的优势菌群包括甲基/乙酸型的甲烷八叠球菌科(Methanosarcinaceae,11%),乙酸型的甲烷鬃菌科(Methanosaetaceae,7.9%)和氢型甲烷菌甲烷杆菌目(Methanomicrobiales,7.4%);公珠错和兹格塘错的优势菌群为甲烷鬃菌科(Methanosaetaceae)分别占15%和15.3%,及甲烷杆菌属(Methanobacterium)和甲基型的甲烷叶菌属(Methanolobus)。公珠错和昆仲错分别以乙酸和甲醇产甲烷速率最高,而兹格塘错从不同底物产甲烷速率无差异。抑制甲烷产生后,公珠错主要积累乙酸,昆仲错主要积累甲醇;兹格塘错不仅甲烷排放低,也无产甲烷物质显著积累。【结论】昆仲错沉积物中的甲烷主要来自甲醇,公珠错中的甲烷主要来自乙酸,而兹格塘错产甲烷和底物积累不活跃。因而推测高原盐碱湖主要的产甲烷途径和菌群可能与周围植被类型的相关性更高,而与盐度的直接相关性较低。     

Fossilized Life in Subseafloor Ultramafic Rocks

Ultramafic rocks are hypothesized to support a subseafloor hydrogen-driven biosphere because of extensive production of bioavailable energy sources like H₂ or CH₄ from fluid-rock interactions. Hence, the apparent lack of microbial remains in subseafloor ultramafic rocks, in contrast to their frequent observation in subseafloor basalts, is somewhat of a paradox. Here we report fossilized microbial remains in aragonite veins in ultramafic rocks from the 15°20′N Fracture Zone area on the Mid-Atlantic Ridge (MAR), collected during Ocean Drilling Program (ODP) Leg 209. The microbial remains consist of filamentous structures associated with biofilms. The young age (<1 Myr) and absence of diagenesis result in fossilized microbial communities with a pristine composition characterized by carbonaceous matter (CM) and the enrichment in trace elements such as Ni, Co, Mo and Mn. Our study confirms the presence of the hypothesized deep subseafloor biosphere hosted in ultramafic rocks. We further show that host rock composition may influence the microbial elemental composition, which is recorded during the fossilization.     

Microbial life associated with low‐temperature alteration of ultramafic rocks in the Leka ophiolite complex

Water–rock interactions in ultramafic lithosphere generate reduced chemical species such as hydrogen that can fuel subsurface microbial communities. Sampling of this environment is expensive and technically demanding. However, highly accessible, uplifted oceanic lithospheres emplaced onto continental margins (ophiolites) are potential model systems for studies of the subsurface biosphere in ultramafic rocks. Here, we describe a microbiological investigation of partially serpentinized dunite from the Leka ophiolite (Norway). We analysed samples of mineral coatings on subsurface fracture surfaces from different depths (10–160 cm) and groundwater from a 50‐m‐deep borehole that penetrates several major fracture zones in the rock. The samples are suggested to represent subsurface habitats ranging from highly anaerobic to aerobic conditions. Water from a surface pond was analysed for comparison. To explore the microbial diversity and to make assessments about potential metabolisms, the samples were analysed by microscopy, construction of small subunit ribosomal RNA gene clone libraries, culturing and quantitative‐PCR. Different microbial communities were observed in the groundwater, the fracture‐coating material and the surface water, indicating that distinct microbial ecosystems exist in the rock. Close relatives of hydrogen‐oxidizing Hydrogenophaga dominated (30% of the bacterial clones) in the oxic groundwater, indicating that microbial communities in ultramafic rocks at Leka could partially be driven by H₂ produced by low‐temperature water–rock reactions. Heterotrophic organisms, including close relatives of hydrocarbon degraders possibly feeding on products from Fischer–Tropsch‐type reactions, dominated in the fracture‐coating material. Putative hydrogen‐, ammonia‐, manganese‐ and iron‐oxidizers were also detected in fracture coatings and the groundwater. The microbial communities reflect the existence of different subsurface redox conditions generated by differences in fracture size and distribution, and mixing of fluids. The particularly dense microbial communities in the shallow fracture coatings seem to be fuelled by both photosynthesis and oxidation of reduced chemical species produced by water–rock reactions.     

Microbial diversity in degraded and non-degraded petroleum samples and comparison across oil reservoirs at local and global scales

Microorganisms have shown their ability to colonize extreme environments including deep subsurface petroleum reservoirs. Physicochemical parameters may vary greatly among petroleum reservoirs worldwide and so do the microbial communities inhabiting these different environments. The present work aimed at the characterization of the microbiota in biodegraded and non-degraded petroleum samples from three Brazilian reservoirs and the comparison of microbial community diversity across oil reservoirs at local and global scales using 16S rRNA clone libraries. The analysis of 620 16S rRNA bacterial and archaeal sequences obtained from Brazilian oil samples revealed 42 bacterial OTUs and 21 archaeal OTUs. The bacterial community from the degraded oil was more diverse than the non-degraded samples. Non-degraded oil samples were overwhelmingly dominated by gammaproteobacterial sequences with a predominance of the genera Marinobacter and Marinobacterium. Comparisons of microbial diversity among oil reservoirs worldwide suggested an apparent correlation of prokaryotic communities with reservoir temperature and depth and no influence of geographic distance among reservoirs. The detailed analysis of the phylogenetic diversity across reservoirs allowed us to define a core microbiome encompassing three bacterial classes (Gammaproteobacteria, Clostridia, and Bacteroidia) and one archaeal class (Methanomicrobia) ubiquitous in petroleum reservoirs and presumably owning the abilities to sustain life in these environments.

     

An Analysis of Respiratory Activity,Q10, and Microbial Community Composition of Soils from High and Low Tussock Sites at Toolik,Alaska

ABSTRACT. High latitude microbial communities, incurring increased global warming, are a potential major source of respiratory CO₂ contributing to an enhanced greenhouse effect. Data on respiration and microbial density are presented for a moist, high tussock site compared with a low, water saturated site. The density of bacteria and eukaryotic microbes was nearly equivalent at both sites and potentially could yield substantial release of respiratory CO₂ with continued warming. Respiratory rates for soil from the high site were greater than the low. The Q₁₀ of 2.4 for the high tussock sample was approximately 1.3 × that of the low site sample (Q₁₀ of 1.7).     

Active microbial ecosystem in Iron-Age tombs of the Etruscan civilization

Earth's microbial biosphere extends down through the crust and much of the subsurface, including those microbial ecosystems located within cave systems. Here, we elucidate the microbial ecosystems within anthropogenic 'caves'; the Iron-Age, subterranean tombs of central Italy. The interior walls of the rock (calcium-rich macco) were painted ~2500 years ago and are covered with CaCO₃ needles (known as moonmilk). The aims of the current study were to: identify biological/geochemical/biophysical determinants of and characterize bacterial communities involved in CaCO₃ precipitation; challenge the maxim that biogenic activity necessarily degrades surfaces; locate the bacterial cells that are the source of the CaCO₃ precipitate; and gain insight into the kinetics of moonmilk formation. We reveal that this environment hosts communities that consist primarily of bacteria that are mesophilic for temperature and xerotolerance (including Actinobacteria, Bacteroidetes and Proteobacteria); is populated by photosynthetic Cyanobacteria exhibiting heterotrophic nutrition (Calothrix and Chroococcidiopsis); and has CaCO₃ precipitating on the rock surfaces (confirmation that this process is biogenic) that acts to preserve rather than damage the painted surface. We also identified that some community members are psychrotolerant (Polaromonas), acidotolerant or acidophilic (members of the Acidobacteria), or resistant to ionizing radiation (Brevundimonas and Truepera); elucidate the ways in which microbiology impacts mineralogy and vice versa; and reveal that biogenic formation of moonmilk can occur rapidly, that is, over a period of 10 to 56 years. We discuss the paradox that these ecosystems, that are for the most part in the dark and lack primary production, are apparently highly active, biodiverse and biomass-rich.     

DOM对米槠次生林不同土层土壤微生物呼吸及其熵值的影响

可溶性有机质(Dissolved organic matter,DOM)作为土壤可溶性有机碳的重要来源,进入土壤之后通过改变土壤微生物数量和活性影响土壤矿化。DOM输入对土壤微生物呼吸和熵值的研究多集中在表层土壤,但对深层土壤微生物呼吸和熵值的影响关注较少。通过室内培养实验(120 d)研究米槠(Castanopsis carlesii)鲜叶DOM添加对表层土壤(0—10 cm)和深层土壤(40—60 cm)微生物呼吸及其土壤代谢熵和微生物熵的影响,为揭示DOM输入对亚热带森林土壤碳过程的影响提供理论依据。结果表明,在培养第1天,添加DOM的表层和深层土壤CO_2瞬时排放速率均显著高于对照(P0.001),分别是对照(不添加DOM)的3.58倍和6.93倍,之后显著下降。就累积排放量而言,无论是DOM添加处理还是对照,表层土壤显著大于深层土壤;在米槠鲜叶DOM添加后,表层土壤累积排放量显著大于对照的表层土壤(P0.001),但DOM添加处理深层土壤累积排放量与对照的深层土壤无明显差异。就微生物生物量碳而言,表层土壤微生物生物量碳含量在培养期间显著大于深层土壤。在整个添加DOM培养期间,表层土壤微生物生物量碳含量显著大于表层对照土壤,深层土壤微生物生物量碳含量显著大于深层对照土壤(第3天除外)。培养结束时(120 d),米槠鲜叶DOM添加处理下,表层土壤和深层土壤有机碳含量与第3天相比分别减少26%和19%。米槠鲜叶DOM添加处理后的深层土壤代谢熵(qCO_2)显著低于对照的深层土壤和DOM添加处理的表层土壤qCO_2(P0.001),说明外源DOM进入深层土壤后提高了土壤微生物对碳的利用效率。米槠鲜叶DOM添加处理后的深层土壤微生物熵是培养第3天的1.58倍,显著大于培养初期(P0.05),而DOM添加处理的表层土壤、对照的表层土壤与深层土壤的微生物熵分别是培养第3天的68%、79%和21%,说明DOM添加提高了深层土壤质量。     

Diverse bacterial groups are associated with corrosive lesions at a Granite Mountain Record Vault (GMRV)

Aims: This study applied culture‐dependent and molecular approaches to examine the bacterial communities at corrosion sites at Granite Mountain Record Vault (GMRV) in Utah, USA, with the goal of understanding the role of microbes in these unexpected corrosion events. Methods and Results: Samples from corroded steel chunks, rock particles and waters around the corrosion pits were collected for bacterial isolation and molecular analyses. Bacteria cultivated from these sites were identified as members of Alphaproteobacteria, Gammaproteobacteria, Firmicutes and Actinobacteria. In addition, molecular genetic characterization of the communities via nested‐polymerase chain reaction‐denaturing gradient gel electrophoresis (DGGE) indicated the presence of a broad spectrum of bacterial groups, including Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. However, neither cultivation nor molecular approaches identified sulfate‐reducing bacteria (SRB), the bacteria commonly implicated as causative organisms were found associated with corrosive lesions in a process referred to as microbially influenced corrosion (MIC). The high diversity of bacterial groups at the corrosion sites in comparison with that seen in the source waters suggested to us a role for the microbes in corrosion, perhaps being an expression of a redox‐active group of microbes transferring electrons, harvesting energy and producing biomass. Conclusions: The corrosion sites contained highly diverse microbial communities, consistent with the involvement of microbial activities along the redox gradient at corrosion interface. We hypothesize an electron transport model for MIC, involving diverse bacterial groups such as acid‐producing bacteria (APB), SRB, sulfur‐oxidizing bacteria (SOB), metal‐reducing bacteria (MRB) and metal‐oxidizing bacteria (MOB). Significance and Impact of the Study: The characterization of micro‐organisms that influence metal‐concrete corrosion at GMRV has significant implications for corrosion control in high‐altitude freshwater environments. MIC provides a potential opportunity to further our understandings of extracellular electron transfer and interspecies communications.     

Microbial diversity and biogeochemistry of the Guaymas Basin deep‐sea hydrothermal plume

Hydrothermal plumes are hot spots of microbial biogeochemistry in the deep ocean, yet little is known about the diversity or ecology of microorganisms inhabiting plumes. Recent biogeochemical evidence shows that Mn(II) oxidation in the Guaymas Basin (GB) hydrothermal plume is microbially mediated and suggests that the plume microbial community is distinct from deep‐sea communities. Here we use a molecular approach to compare microbial diversity in the GB plume and in background deep seawater communities, and cultivation to identify Mn(II)‐oxidizing bacteria from plumes and sediments. Despite dramatic differences in Mn(II) oxidation rates between plumes and background seawater, microbial diversity and membership were remarkably similar. All bacterial clone libraries were dominated by Gammaproteobacteria and archaeal clone libraries were dominated by Crenarchaeota. Two lineages, both phylogenetically related to methanotrophs and/or methylotrophs, were consistently over‐represented in the plume. Eight Mn(II)‐oxidizing bacteria were isolated, but none of these or previously identified Mn(II) oxidizers were abundant in clone libraries. Taken together with Mn(II) oxidation rates measured in laboratory cultures and in the field, these results suggest that Mn(II) oxidation in the GB hydrothermal plume is mediated by genome‐level dynamics (gene content and/or expression) of microorganisms that are indigenous and abundant in the deep sea but have yet to be unidentified as Mn(II) oxidizers.