Methanotrophs of the Psychrophilic Microbial Community of the Russian Arctic Tundra

In tundra, at a low temperature, there exists a slowly developing methanotrophic community. Methane-oxidizing bacteria are associated with plants growing at high humidity, such as sedge and sphagnum; no methanotrophs were found in polytrichous and aulacomnious mosses and lichens, typical of more arid areas. The methanotrophic bacterial community inhabits definite soil horizons, from moss dust to peat formed from it. The potential ability of the methanotrophic community to oxidize methane at 5°C enhances with the depth of the soil profile in spite of the decreasing soil temperature. The methanotrophic community was found to gradually adapt to various temperatures due to the presence of different methane-oxidizing bacteria in its composition. Depending on the temperature and pH, different methanotrophs occupy different econiches. Within a temperature range from 5 to 15°C, three morphologically distinct groups of methanotrophs could be distinguished. At pH 5–7 and 5–15°C, forms morphologically similar to Methylobacter psychrophilus predominated, whereas at the acidic pH 4–6 and 10–15°C, bipolar cells typical of Methylocella palustris were mostly found. The third group of methanotrophic bacteria growing at pH 5–7 and 5–10°C was represented by a novel methanotroph whose large coccoid cells had a thick mucous capsule.     

Quantitative 3D Model of Light Transmittance Through Translucent Rocks Applied to the Hypolithic Microbial Community

In extreme desert environments, photosynthetic microorganisms often live on the buried undersides of translucent rocks. Computing the light level reaching these locations requires 3D modeling of a finite rock. We report on Monte Carlo calculations of skylight and sunlight transmission through a partially buried flat cylindrical rock using one billion photons per simulation. Transmitted light level drops inversely with increasing rock opacity, as expected for purely scattering media. For a half-buried rock with an extinction coefficient of 0.1 cm^?1 (opacity of 0.2), transmission at the bottom is 64 % for sunlight at a solar zenith angle of 60° and 82 % for skylight. Transmitted light level increases slowly with increasing scattering asymmetry factor of the rock independent of illumination or depth buried. Transmitted sunlight at zenith through a thick half-buried rock (opacity of 0.6) is six times brighter at the bottom than the subsurface sides. Skylight transmits equally to the subsurface sides and bottom. When the sun is not straight overhead, the sunward side of the rock is brighter than the underside of the rock. Compared to the sunlight transmitted to the bottom, transmitted sunlight inclined at 60° is 24 times brighter at the subsurface side towards the sun and 14 times brighter at the subsurface side 70° away from the sun. Transmitted sunlight emitted from zenith and skylight is uniformly bright at the bottom regardless of how deeply the rock is buried. Sunlight not at zenith transmits preferentially to the sunward bottom edge depending on the depth the rock is buried.     

Regulation of Microbial Community Composition and Activity by Soil Nutrient Availability, Soil pH, and Herbivory in the Tundra

Soil nitrogen (N) availability and pH constitute major abiotic controls over microbial community composition and activity in tundra ecosystems. On the other hand, mammalian grazers form an important biotic factor influencing resource coupling between plants and soil microorganisms. To investigate individual effects and interactions among soil nutrients, pH, and grazing on tundra soils, we performed factorial treatments of fertilization, liming, and grazer exclusion in the field for 3 years at 2 contrasting tundra habitats, acidic (N-poor) and non-acidic (N-rich) tundra heaths. The effects of all treatments were small in the non-acidic tundra heaths. In the acidic tundra heaths, fertilization decreased the fungal:bacterial ratio as analyzed by soil PLFAs, but there were no effects of liming. Fertilization increased soil N concentrations more drastically in ungrazed than grazed plots, and in parallel, fertilization decreased the fungal:bacterial ratio to a greater extent in the ungrazed plots. Liming, on the other hand, partly negated the effects of fertilization on both soil N concentrations and PLFAs. Fertilization drastically increased the activity of phenol oxidase, a microbial enzyme synthesized for degradation of soil phenols, in grazed plots, but had no effect in ungrazed plots. Taken together, our results demonstrate that grazers have the potential to regulate the fungal:bacterial ratio in soils through influencing N availability for the soil microorganisms.     

Hypolithic Cyanobacteria, Dry Limit of Photosynthesis, and Microbial Ecology in the Hyperarid Atacama Desert

The occurrence of hypolithic cyanobacteria colonizing translucent stones was quantified along the aridity gradient in the Atacama Desert in Chile, from less arid areas to the hyperarid core where photosynthetic life and thus primary production reach their limits. As mean rainfall declines from 21 to ≤2 mm year⁻¹, the abundance of hypolithic cyanobacteria drops from 28 to <0.1%, molecular diversity declines threefold, and organic carbon residence times increase by three orders of magnitude. Communities contained a single Chroococcidiopsis morphospecies with heterotrophic associates, yet molecular analysis revealed that each stone supported a number of unique 16S rRNA gene-defined genotypes. A fivefold increase in steady-state residence times for organic carbon within communities in the hyperarid core (3200 years turnover time) indicates a significant decline in biological carbon cycling. Six years of microclimate data suggest that the dry limit corresponds to ≤5 mm year⁻¹ rainfall and/or decadal periods of no rain, with <75 h year⁻¹ of liquid water available to cyanobacteria under light conditions suitable for photosynthesis. In the hyperarid core, hypolithic cyanobacteria are rare and exist in small spatially isolated islands amidst a microbially depauperate bare soil. These findings suggest that photosynthetic life is extremely unlikely on the present-day surface of Mars, but may have existed in the past. If so, such microhabitats would probably be widely dispersed, difficult to detect, and millimeters away from virtually lifeless surroundings.     

The Role of Thermal Regime in Tundra Plant Community Restoration

Mineral extraction activities in the Arctic regions of the world produce long-lasting ecological disturbances. Assisted recovery from such disturbances may require restoration of the tundra thermal regime. We transplanted plugs of entire root zone and live tundra plants to a disturbed site in Alaska oil fields. The dominant species were Carex aquatilis, Eriophorum angustifolium, Dupontia fisheri, Poa glauca, Festuca rubra, Salix ovalifolia, S. reticulata, and Sphagnum spp. We studied plant responses in the plugs to thermal regime manipulations by means of greenhouse and of single- or double-plug treatments. All plugs continued to produce new plants with time and expanded in area and canopy volume. Plants responded differently to treatments and generally reversed those responses when we reversed the greenhouse treatment the third year after transplant. Our small-scale experiment showed that the native thermal regime of a plant community is vital in revegetating a disturbed tundra. But large-scale restoration using transplants requires resources of modern extraction technology, engineering, and planning to salvage the extensive live tundra mats now routinely destroyed under gravel fills of roads, structures, and mine-site stockpiles.     

Actinobacterial Diversity in Microbial Mats of Five Hot Springs in Central and Central-Eastern Tibet,China

The diversity and community composition of Actinobacteria in microbial mats of five Tibetan hot springs (temperatures 26°C to 81°C) and a sympatric soil were investigated with 16S rRNA gene phylogentic analysis. A total of 278 clones were obtained. The actinobacterial communities in the Tibetan hot springs were diverse, and most of the retrieved clones were affiliated with Actinobacteridae, Acidimicrobidae, and unclassified Actinobacteria. The Actinobacteridae sequences were distributed into seven suborders (e.g., Frankineae, Corynebacterineae, Micromonosporineae, Pseudonocardineae, Propionibacterineae, Micrococcineae, and Actinomycineae) and unclassified Actinobacteridae. The actinobacterial composition varied among different hot springs. Statistical analysis showed that the actinobacterial diversity in the investigated Tibetan hot springs was not significantly correlated with temperature, suggesting that temperature is not a key factor in shaping the actinobacterial diversity in hot springs.     

Microbial Iron Oxidation in the Arctic Tundra and Its Implications for Biogeochemical Cycling

The role that neutrophilic iron-oxidizing bacteria play in the Arctic tundra is unknown. This study surveyed chemosynthetic iron-oxidizing communities at the North Slope of Alaska near Toolik Field Station (TFS) at Toolik Lake (lat 68.63, long −149.60). Microbial iron mats were common in submerged habitats with stationary or slowly flowing water, and their greatest areal extent is in coating plant stems and sediments in wet sedge meadows. Some Fe-oxidizing bacteria (FeOB) produce easily recognized sheath or stalk morphotypes that were present and dominant in all the mats we observed. The cool water temperatures (9 to 11°C) and reduced pH (5.0 to 6.6) at all sites kinetically favor microbial iron oxidation. A microbial survey of five sites based on 16S rRNA genes found a predominance of Proteobacteria, with Betaproteobacteria and members of the family Comamonadaceae being the most prevalent operational taxonomic units (OTUs). In relative abundance, clades of lithotrophic FeOB composed 5 to 10% of the communities. OTUs related to cyanobacteria and chloroplasts accounted for 3 to 25% of the communities. Oxygen profiles showed evidence for oxygenic photosynthesis at the surface of some mats, indicating the coexistence of photosynthetic and FeOB populations. The relative abundance of OTUs belonging to putative Fe-reducing bacteria (FeRB) averaged around 11% in the sampled iron mats. Mats incubated anaerobically with 10 mM acetate rapidly initiated Fe reduction, indicating that active iron cycling is likely. The prevalence of iron mats on the tundra might impact the carbon cycle through lithoautotrophic chemosynthesis, anaerobic respiration of organic carbon coupled to iron reduction, and the suppression of methanogenesis, and it potentially influences phosphorus dynamics through the adsorption of phosphorus to iron oxides.     

Molecular Characterization of an Endolithic Microbial Community in Dolomite Rock in the Central Alps (Switzerland)

Endolithic microorganisms colonize the pores in exposed dolomite rocks in the Piora Valley in the Swiss Alps. They appear as distinct grayish-green bands about 1–8 mm below the rock surface. Based on environmental small subunit ribosomal RNA gene sequences, a diverse community driven by photosynthesis has been found. Cyanobacteria (57 clones), especially the genus Leptolyngbya, form the functional basis for an endolithic community which contains a wide spectrum of so far not characterized species of chemotrophic Bacteria (64 clones) with mainly Actinobacteria, Alpha-Proteobacteria, Bacteroidetes, and Acidobacteria, as well as a cluster within the Chloroflexaceae. Furthermore, a cluster within the Crenarchaeotes (40 clones) has been detected. Although the eukaryotic diversity was outside the scope of the study, an amoeba (39 clones), and several green algae (51 clones) have been observed. We conclude that the bacterial diversity in this endolithic habitat, especially of chemotrophic, nonpigmented organisms, is considerable and that Archaea are present as well.     

Improving the Shear Strength of Quartz Sand using the Microbial Method

An increase in urban population and the reduced number of suitable lands for construction projects have necessitated the need for ground improvement methods with no environmentally detrimental effects. Microbial-induced calcite precipitation (MICP) is a relatively environmentally friendly method for soil regeneration. In the present paper, X-ray diffraction (XRD) and scanning electron microscopy (SEM) analyses were performed to investigate the type and method of cement formation in loose quartz sand with different densities stabilized using bacteria. The results showed that the highest content of calcium carbonate cement was produced in the sample with the lowest density. Moreover, after microbial stabilization, the shear strength measured in the direct shear test was increased in the specimen with a lower density. We observed an increase in shear strength from 0.63 kg/cm² before injection for loose sand (γ = 1.5 g/cm³) to 3.92 kg/cm² after injection. In addition, the effect of injection time was investigated and found that shear strength in the two-stage injection per day is greater than that in one- and three-stage injections per day. With prolonging the injection time from one to five days, shear strength was significantly increased from 2.07 to 4.54 kg/cm². Furthermore, prolonging the bacterial treatment period led to a significant increase in the produced carbonate cement and, consequently, enhanced soil shear strength.     

Central Role of the Cell in Microbial Ecology

Summary: Over the last few decades, advances in cultivation-independent methods have significantly contributed to our understanding of microbial diversity and community composition in the environment. At the same time, cultivation-dependent methods have thrived, and the growing number of organisms obtained thereby have allowed for detailed studies of their physiology and genetics. Still, most microorganisms are recalcitrant to cultivation. This review not only conveys current knowledge about different isolation and cultivation strategies but also discusses what implications can be drawn from pure culture work for studies in microbial ecology. Specifically, in the light of single-cell individuality and genome heterogeneity, it becomes important to evaluate population-wide measurements carefully. An overview of various approaches in microbial ecology is given, and the cell as a central unit for understanding processes on a community level is discussed.     

Diverse UV-B Resistance of Culturable Bacterial Community from High-Altitude Wetland Water

Isolation of most ultraviolet B (UV-B)-resistant culturable bacteria that occur in the habitat of Laguna Azul, a high-altitude wetland [4554 m above sea level (asl)] from the Northwestern Argentinean Andes, was carried out by culture-based methods. Water from this environment was exposed to UV-B radiation under laboratory conditions during 36 h, at an irradiance of 4.94 W/m². It was found that the total number of bacteria in water samples decreased; however, most of the community survived long-term irradiation (312 nm) (53.3 kJ/m²). The percentage of bacteria belonging to dominant species did not vary significantly, depending on the number of UV irradiation doses. The most resistant microbes in the culturable community were Gram-positive pigmented species (Bacillus megaterium [endospores and/or vegetative cells], Staphylococcus saprophyticus, and Nocardia sp.). Only one Gram-negative bacterium could be cultivated (Acinetobacter johnsonii). Nocardia sp. that survived doses of 3201 kJ/m² were the most resistant bacteria to UV-B treatment. This study is the first report on UV-B resistance of a microbial community isolated from high-altitude extreme environments, and proposes a method for direct isolation of UV-B-resistant bacteria from extreme irradiated environments. This article is dedicated to the memory of Carolina Colin.     

Organic Layer Serves as a Hotspot of Microbial Activity and Abundance in Arctic Tundra Soils

Tundra ecosystem is of importance for its high accumulation of organic carbon and vulnerability to future climate change. Microorganisms play a key role in carbon dynamics of the tundra ecosystem by mineralizing organic carbon. We assessed both ecosystem process rates and community structure of Bacteria, Archaea, and Fungi in different soil layers (surface organic layer and subsurface mineral soil) in an Arctic soil ecosystem located at Spitsbergen, Svalbard during the summer of 2008 by using biochemical and molecular analyses, such as enzymatic assay, terminal restriction fragment length polymorphism (T-RFLP), quantitative polymerase chain reaction (qPCR), and pyrosequencing. Activity of hydrolytic enzymes showed difference according to soil type. For all three microbial communities, the average gene copy number did not significantly differ between soil types. However, archaeal diversities appeared to differ according to soil type, whereas bacterial and fungal diversity indices did not show any variation. Correlation analysis between biogeochemical and microbial parameters exhibited a discriminating pattern according to microbial or soil types. Analysis of the microbial community structure showed that bacterial and archaeal communities have different profiles with unique phylotypes in terms of soil types. Water content and hydrolytic enzymes were found to be related with the structure of bacterial and archaeal communities, whereas soil organic matter (SOM) and total organic carbon (TOC) were related with bacterial communities. The overall results of this study indicate that microbial enzyme activity were generally higher in the organic layer than in mineral soils and that bacterial and archaeal communities differed between the organic layer and mineral soils in the Arctic region. Compared to mineral soil, peat-covered organic layer may represent a hotspot for secondary productivity and nutrient cycling in this ecosystem.     

Post-Fire Population Dynamics of Two Tree Species in High-Altitude Polylepis Forests of Central Ecuador

Fire is considered the main cause for the patchy distribution of high-montane tropical forests growing below the upper limit of tree growth, but there are little quantitative data on the impacts of burning on the respective tree populations. This study compares adult tree survival as well as sapling (0.05–1.3 m) and seedling (<0.05 m) recruitment of Polylepis incana , and the coexisting Gynoxis acostae in burned and unburned forest stands in the Páramo de Guamaní, central Ecuador. In P. incana , adult survival after burning was low, whereas all G. acostae individuals survived through resprouting. Two years after fire, the density of P. incana seedlings and saplings was higher than that of G. acostae , but still not sufficient for forest recovery. A sowing experiment revealed a significantly lower seedling emergence of both species in the burned than in the unburned plots. Seedling emergence was comparable to laboratory studies performed under optimal conditions, suggesting there was no evidence for climate constraining emergence at the given altitude. Interactions between seedling survival and burning for P. incana indicate higher seedling survival after burning, which could not be shown for G. acostae . Our data imply that single fire events strongly decrease adult and seedling population sizes in P. incana and thus may be the main reason for the discontinuous forest distribution below the upper distribution limit of the species. In contrast, the high resprouting potential of G. acostae explains its relatively high percentage in the remaining Ecuadorian P. incana stands.     

长白山苔原植被变化对土壤呼吸影响研究

气候变化导致长白山苔原由灌木苔原向灌草苔原演化,对土壤呼吸及碳循环造成了重要影响。为了明确植被变化对苔原土壤呼吸的影响,该研究选取了长白山苔原典型的群落,测定分析了不同草本植物盖度下的土壤呼吸的季节动态变化及差异。结果表明：(1)在生长季,3个群落下不同变化阶段样地的土壤呼吸速率均有明显的动态变化,均呈单峰型变化特征;草本植物盖度增加没有改变土壤呼吸的季节动态变化趋势。(2)草本植物盖度增加对土壤呼吸速率有显著影响,随着草本植物盖度的增加,土壤呼吸速率也逐渐增大。(3)不同植物群落下土壤呼吸不同,在草本植物盖度相同的条件下土壤呼吸速率依次为：牛皮杜鹃 小叶章群落>牛皮杜鹃 地榆群落>笃斯越桔 苔草群落。(4)不同群落草本植物盖度增加对土壤呼吸的增速效应不同,牛皮杜鹃 小叶章群落的土壤呼吸增速最快,笃斯越桔 苔草群落的次之,牛皮杜鹃 地榆群落最小;草本植物盖度的增加也使3个群落之间土壤呼吸的差值出现明显的变化。     

Increased Above- and Belowground Plant Input Can Both Trigger Microbial Nitrogen Mining in Subarctic Tundra Soils

Ecosystems - Low nitrogen (N) availability in the Arctic and Subarctic constrains plant productivity, resulting in low litter inputs to soil. Increased N availability and litter inputs as a result...     

Nitrogen-Cycling Genes in Epilithic Biofilms of Oligotrophic High-Altitude Lakes (Central Pyrenees,Spain)

Microbial biofilms in oligotrophic environments are the most reactive component of the ecosystem. In high-altitude lakes, exposed bedrock, boulders, gravel, and sand in contact with highly oxygenated water and where a very thin epilithic biofilm develops usually dominate the littoral zone. Traditionally, these surfaces have been considered unsuitable for denitrification, but recent investigations have shown higher biological diversity than expected, including diverse anaerobic microorganisms. In this study, we explored the presence of microbial N-cycling nirS and nirK (denitrification through the conversion of NO₂ ^? to NO), nifH (N₂ fixation), anammox (anaerobic ammonium oxidation), and amoA (aerobic ammonia oxidation, both bacterial and archaeal) genes in epilithic biofilms of a set of high-altitude oligotrophic lakes in the Pyrenees. The concentrations of denitrifying genes determined by quantitative PCR were two orders of magnitude higher than those of ammonia-oxidizing genes. Both types of genes were significantly correlated, suggesting a potential tight coupling nitrification-denitrification in these biofilms that deserves further confirmation. The nifH gene was detected after nested PCR, and no signal was detected for the anammox-specific genes used. The taxonomic composition of denitrifying and nitrogen-fixing genes was further explored by cloning and sequencing. Interestingly, both microbial functional groups were richer and more genetically diverse than expected. The nirK gene, mostly related to Alphaproteobacteria (Bradyrhizobiaceae), dominated the denitrifying gene pool as expected for oxygen-exposed habitats, whereas Deltaproteobacteria (Geobacter like) and Cyanobacteria were the most abundant among nitrogen fixers. Overall, these results suggest an epilithic community more metabolically diverse than previously thought and with the potential to carry out an active role in the biogeochemical nitrogen cycling of high-altitude ecosystems. Measurements of activity rates should be however carried out to substantiate and further explore these findings.     

Biolog方法在环境微生物群落研究中的应用

环境微生物群落研究具有非常重要的理论和应用价值。本文介绍了一种测定微生物代谢的Ｂｉｏｌｏｇ微平板法 ,以及这种新方法在环境微生物群落研究方面的应用成果。1　环境微生物群落研究的意义与手段1 .1　环境微生物群落的研究内容环境微生物是由多个种群 (ｐｏｐｕｌａｔｉｏｎ)组成的微生物群落 (ｃｏｍｍｕｎｉｔｙ) ,不同种群之间存在着共生、互利、共存、竞争等各种复杂的关系 ,在物质循环和能量转化过程中发挥着重要作用。对环境微生物群落的研究可以从微生物的量 ,代谢活性 ,群落结构及代谢功能等几个不同层面上进行。其中 ,微生物…     

Tylenchulus semipenetrans Alters the Microbial Community in the Citrus Rhizosphere

Infection of citrus seedlings by Tylenchulus semipenetrans was shown to reduce subsequent infection of roots by Phytophthora nicotianae and to increase plant growth compared to plants infected by only the fungus. Hypothetical mechanisms by which the nematode suppresses fungal development include nutrient competition, direct antibiosis, or alteration of the microbial community in the rhizosphere to favor microorganisms antagonistic to P. nicotianae. A test of the last hypothesis was conducted via surveys of five sites in each of three citrus orchards infested with both organisms. A total of 180 2-cm-long fibrous root segments, half with a female T. semipenetrans egg mass on the root surface and half without, were obtained from each orchard site. The samples were macerated in water, and fungi and bacteria in the suspensions were isolated, quantified, and identified. No differences were detected in the numbers of microorganism species isolated from nematode-infected and uninfected root segments. However, nematode-infected root segments had significantly more propagules of bacteria at all orchard sites. Bacillus megaterium and Burkholderia cepacia were the dominant bacterial species recovered. Bacteria belonging to the genera Arthrobacter and Stenotrophomonas were encountered less frequently. The fungus community was dominated by Fusarium solani, but Trichoderma, Verticillum, Phythophthora, and Penicillium spp. also were recovered. All isolated bacteria equally inhibited the growth of P. nicotianae in vitro. Experiments using selected bacteria, T. semipenetrans, and P. nicotianae, alone or in combination, were conducted in both the laboratory and greenhouse. Root and stem fresh weights of P. nicotianae-infected plants treated with T. semipenetrans, B. cepacia, or B. megaterium were greater than for plants treated only with the fungus. Phytophthora nicotianae protein in roots of fungus-infected plants was reduced by nematodes (P ≤ 0.001), either alone or in combination with either bacterium. However, treatment with bacteria did not affect P. nicotianae development in roots. The results suggest different mechanisms by which T. semipenetrans, B. cepacia, and B. megaterium may mitigate virulence of P. nicotianae.