The first results of a study of the phylogenetic diversity of microorganisms in southern Baikal sediments from the area of subsurface depositions of methane hydrates

Phylogenetic analysis of the bacterial communities in Lake Baikal bottom sediments in the region of subsurface methane hydrate depositions has been carried out using data on 16S rRNA sequences. The composition of these microbial communities is shown to be different in different horizons. Methanotrophic bacteria are found in the surface layer (0-5 cm), and uncultured bacteria constitute a great portion of this population. In deeper sediment layers (92-96 cm), achange in the microbial community occurs; specifically, a decreased homology with the known sequences is observed. The new sequences form separate clusters on a phylogenetic tree, indicating the possibly endemic nature of the bacteria revealed. Organisms related to the genus Pseudomonas constitute the main portion of the population. An archaea-related sequence was found in a horizon containing gas hydrate crystals (100-128 cm). Uncultured bacteria remain predominant.     

Microbiological and chemical properties of soil associated with macropores at different depths in a red-duplex soil in NSW Australia

Some agricultural soils in South Eastern Australia with duplex profiles have subsoils with high bulk density, which may limit root penetration, water uptake and crop yield. In these soils, a large proportion (up to 80%) of plant roots maybe preferentially located within the macropores or in the soil within 1–10 mm of the macropores, a zone defined as the macropore sheath (MPS). The chemical and microbiological properties of MPS soil manually dissected from a 1–3 mm wide region surrounding the macropores was compared with that of adjacent bulk soil (>10 mm from macropores) at 4 soil depths (0–20 cm, 20–40 cm, 40–60 cm and 60–80 cm). Compared to the bulk soil, the MPS soil had higher organic C, total N, bicarbonate-extractable P, Ca⁺, Cu, Fe and Mn and supported higher populations of bacteria, fungi, actinomycetes, Pseudomonas spp., Bacillus spp., cellulolytic bacteria, cellulolytic fungi, nitrifying bacteria and the root pathogen Pythium.In addition, analysis of carbon substrate utilization patterns showed the microbial community associated with the MPS soil to have higher metabolic activity and greater functional diversity than the microbial community associated with the bulk soil at all soil depths. Phospholipid fatty acids associated with bacteria and fungi were also shown to be present in higher relative amounts in the MPS soil compared to the bulk soil. Whilst populations of microbial functional groups in the MPS and the bulk soil declined with increasing soil depth, the differentiation between the two soils in microbiological properties occurred at all soil depths. Soil aggregates (< 0.5 mm diameter) associated with plant roots located within macropores were found to support a microbial community that was quantitatively and functionally different to that in the MPS soil and the bulk soil at all soil depths. The microbial community associated with these soil aggregates thus represented a third recognizable environment for plant roots and microorganisms in the subsoil.     

Responses of Soil Microbial Communities to Experimental Warming in Alpine Grasslands on the Qinghai-Tibet Plateau

Global surface temperature is predicted to increase by at least 1.5°C by the end of this century. However, the response of soil microbial communities to global warming is still poorly understood, especially in high-elevation grasslands. We therefore conducted an experiment on three types of alpine grasslands on the Qinghai-Tibet Plateau to study the effect of experimental warming on abundance and composition of soil microbial communities at 0–10 and 10–20 cm depths. Plots were passively warmed for 3 years using open-top chambers and compared to adjacent control plots at ambient temperature. Soil microbial communities were assessed using phospholipid fatty acid (PLFA) analysis. We found that 3 years of experimental warming consistently and significantly increased microbial biomass at the 0–10 cm soil depth of alpine swamp meadow (ASM) and alpine steppe (AS) grasslands, and at both the 0–10 and 10–20 cm soil depths of alpine meadow (AM) grasslands, due primarily to the changes in soil temperature, moisture, and plant coverage. Soil microbial community composition was also significantly affected by warming at the 0–10 cm soil depth of ASM and AM and at the 10–20 cm soil depth of AM. Warming significantly decreased the ratio of fungi to bacteria and thus induced a community shift towards bacteria at the 0–10 cm soil depth of ASM and AM. While the ratio of arbuscular mycorrhizal fungi to saprotrophic fungi (AMF/SF) was significantly decreased by warming at the 0–10 cm soil depth of ASM, it was increased at the 0–10 cm soil depth of AM. These results indicate that warming had a strong influence on soil microbial communities in the studied high-elevation grasslands and that the effect was dependent on grassland type.     

Distribution of Microorganisms in the Al–Fe–Humus Podzols of Natural and Anthropogenically Impacted Boreal Spruce Forests

Natural and anthropogenically induced seasonal variations in the abundance and biomass of various groups of microorganisms in the Al–Fe–humus podzols of boreal spruce forests were analyzed. The fungal biomass in these soils was found to be considerably higher than the bacterial biomass. The microbial population was mainly concentrated in a thin surface layer (10–15 cm in thickness), which included the forest litter and the upper mineral root-inhabited soil horizon and greatly differed from other soil horizons in morphology and other properties. This layer was found to be optimal with respect to hydrothermal and nutritional conditions and is characterized by profound seasonal variations in the abundance and biomass of microbiota. The high acidity, typical of the Al–Fe–humus podzols, resulted from the metabolism of their microbial communities. In the polluted podzols, the population of prokaryotes increased and that of eukaryotes decreased.     

Structure and seasonal dynamics of hyporheic zone microbial communities in free-stone rivers of the estern United States

The hyporheic zone of a river is characterized by being nonphotic, exhibiting chemical/redox gradients, and having a heterotrophic food web based on the consumption of organic carbon entrained from surface waters. Hyporheic microbial communities constitute the base of food webs in these environments and are important for maintaining a functioning lotic ecosystem. While microbial communities of rivers dominated by fine-grained sediments are relatively well studied, little is known about the structure and seasonal dynamics of microbial communities inhabiting the predominantly gravel and cobble hyporheic zones of rivers of the western United States. Here, we present the first molecular analysis of hyporheic microbial communities of three different stream types (based on mean base discharge, substratum type, and drainage area), in Montana. Utilizing 16S rDNA phylogeny, DGGE pattern analysis, and qPCR, we have analyzed the prokaryotic communities living on the 1.7 to 2.36 mm grain-size fraction of hyporheic sediments from three separate riffles in each stream. DGGE analysis showed clear seasonal community patterns, indicated similar community composition between different riffles within a stream (95.6–96.6% similarity), and allowed differentiation between communities in different streams. Each river supported a unique complement of species; however, several phylogenetic groups were conserved between all three streams including Pseudomonads and members of the genera Aquabacterium, Rhodoferax, Hyphomicrobium, and Pirellula. Each group showed pronounced seasonal trends in abundance, with peaks during the Fall. The Hyphomicrobium group was numerically dominant throughout the year in all three streams. This work provides a framework for investigating the effects of various environmental factors and anthropogenic effects on microbial communities inhabiting the hyporheic zone.     

Change in microbial communities in acetate- and glucose-fed microbial fuel cells in the presence of light

Power densities produced by microbial fuel cells (MFCs) in natural systems are changed by exposure to light through the enrichment of photosynthetic microorganisms. When MFCs with brush anodes were exposed to light (4000 lx), power densities increased by 8–10% for glucose-fed reactors, and 34% for acetate-fed reactors. Denaturing gradient gel electrophoresis (DGGE) profiles based on the 16S rRNA gene showed that exposure to high light levels changed the microbial communities on the anodes. Based on 16S rRNA gene clone libraries of light-exposed systems the anode communities using glucose were also significantly different than those fed acetate. Dominant bacteria that are known exoelectrogens were identified in the anode biofilm, including a purple nonsulfur (PNS) photosynthetic bacterium, Rhodopseudomonas palustris, and a dissimilatory iron-reducing bacterium, Geobacter sulfurreducens. Pure culture tests confirmed that PNS photosynthetic bacteria increased power production when exposed to high light intensities (4000 lx). These results demonstrate that power production and community composition are affected by light conditions as well as electron donors in single-chamber air-cathode MFCs.     

Effects of agronomical measures on the microbial diversity of soils as related to the suppression of soil-borne plant pathogens

The diversity of soil microbial communities can be key to the capacity of soils tosuppress soil-borne plant diseases. As agricultural practice, as well as directedagronomical measures, are known to be able to affect soil microbial diversity, it isplausible that the soil microflora can be geared towards a greater suppressivity ofsoil-borne diseases as a result of the selection of suitable soil management regimes.In the context of a programme aimed at investigating the microbial diversity of soilsunder different agricultural regimes, including permanent grassland versus arableland under agricultural rotation, we assessed how soil microbial diversity is affectedin relation to the suppression of the soil-borne potato pathogen Rhizoctoniasolani AG3. The diversity in the microbial communities over about a growingseason was described by using cultivation-based – plating on different media – and cultivation-independent – soil DNA-based PCR followed by denaturing gradient gel electrophoresis (DGGE) community fingerprinting – methods. The results showed great diversity in the soil microbiota at both the culturable and cultivation-independent detection levels. Using cultivation methods, various differences between treatments with respect to sizes of bacterial and fungal populations were detected, with highest population sizes generally found in rhizospheres. In addition, the evenness of eco-physiologically differing bacterial types was higher in grassland than in arable land under rotation. At the cultivation-independent level, clear differences in the diversities of several microbial groups between permanent grassland and arable land under rotation were apparent. Bio-assays that assessed the growth of R. solani AG3 hyphae through soil indicated a greater growth suppression in grassland than in arable land soils. Similarly, an experiment performed in the glasshouse showed clear differences in both microbial diversities and suppressiveness of R. solani growth in soil, depending on the presence of either maizeor oats as the crop. The significance of these findings for designing soil managementstrategies is discussed.     

Monitoring of microbial community structure and succession in the biohydrogen production reactor by denaturing gradient gel electrophoresis (DGGE)

To study the structure of microbial communities in the biological hydrogen production reactor and determine the ecological function of hydrogen producing bacteria, anaerobic sludge was obtained from the continuous stirred tank reactor (CSTR) in different periods of time, and the diversity and dynamics of microbial communities were investigated by denaturing gradient gel electrophoresis (DGGE). The results of DGGE demonstrated that an obvious shift of microbial population happened from the beginning of star-up to the 28th day, and the ethanol type fermentation was established. After 28 days the structure of microbial community became stable, and the climax community was formed. Comparative analysis of 16S rDNA sequences from reamplifying and sequencing the prominent bands indicated that the dominant population belonged to low G+C Gram-positive bacteria (Clostridium sp. andEthanologenbacterium sp.), β-proteobacteria (Acidovorax sp.), γ-proteobacteria (Kluyvera sp.), Bacteroides (uncultured bacterium SJA-168), and Spirochaetes (uncultured eubacterium E1-K13), respectively. The hydrogen production rate increased obviously with the increase ofEthanologenbacterium sp.,Clostridium sp. and uncultured Spirochaetes after 21 days, meanwhile the succession of ethanol type fermentation was formed. Throughout the succession the microbial diversity increased however it decreased after 21 days. Some types ofClostridium sp.Acidovorax sp.,Kluyvera sp., and Bacteroides were dominant populations during all periods of time. These special populations were essential for the construction of climax community. Hydrogen production efficiency was dependent on both hydrogen producing bacteria and other populations. It implied that the cometabolism of microbial community played a great role of biohydrogen production in the reactors.     

A Technique To Quantify the Population Size and Composition of the Biofilm Component in Communities of Bacteria in the Phyllosphere

The presence of microbial biofilms in the phyllosphere of terrestrial plants has recently been demonstrated, but few techniques to study biofilms associated with living plant tissues are available. Here we report a technique to estimate the proportion of the bacterial population on leaves that is assembled in biofilms and to quantitatively isolate bacteria from the biofilm and nonbiofilm (solitary) components of phyllosphere microbial communities. This technique is based on removal of bacteria from leaves by gentle washing, separation of biofilm and solitary bacteria by filtration, and disintegration of biofilms by ultrasonication. The filters used for this technique were evaluated for their nonspecific retention rates of solitary bacteria and for the efficiency of filtration for different concentrations of solitary bacteria in the presence of biofilms and other particles. The lethality and efficiency of disintegration of the sonication conditions used here were also evaluated. Isolation and quantification of bacteria by this technique is based on use of culture media. However, oligonucleotide probes, sera, or epifluorescent stains could also be used for direct characterization of the biofilm and solitary bacteria in the suspensions generated by this technique. Preliminary results from estimates of biofilm abundance in phyllosphere communities show that bacteria in biofilms constitute between about 10 and 40% of the total bacterial population on broad-leaf endive and parsley leaves.     

Monitoring of microbial community structure and succession in the biohydrogen production reactor by denaturing gradient gel electrophoresis (DGGE)

Biohydrogen production has been concerned ex-tremely as a new technology of energy resource pro-duction by many scientists[1—4]. Enhancement of hy-drogen production efficiency and cutting down the operating cost are very important problems, which are the limiting factors for the industrialization of hydro-gen production process. The fermentation hydrogen production technology offers a new method to resolve these difficulties[5—8]. Compared with photosynthetic hydrogen production possesses, f…     

The variation of soil microbial respiration with depth in relation to soil carbon composition

The vertical variation in soil microbial respiratory activity and its relationship to organic carbon pools is critical for modeling soil C stock and predicting impacts of climate change, but is not well understood. Mineral soil samples, taken from four Scottish soils at different depths (0–8, 8–16, 16–24, 24–32 cm), were analyzed and incubated in the laboratory under constant temperature and environmental conditions. The vegetation type/plant species showed significant effects on the absolute concentration of C components and microbial activity, but the relative distribution of C and respiration rate with soil depth are similar across sites. Soil C pools and microbial respiratory activity declined rapidly with soil depth, with about 30% of total organic carbon (TOC) and dissolved organic carbon (DOC), and about half microbial carbon (C_mic) and respired CO₂ observed in the top 8 cm. The ratio of CO₂:TOC generally decreased with soil depth, but CO₂:DOC was significantly higher in the top 8 cm of soil than in the subsoil (8–32 cm). No general pattern between qCO₂ (CO₂:C_mic) and soil depth was found. The vertical distributions of soil C pools and microbial respiratory activity were best fitted with a single exponential equation. Compared with TOC and DOC, C_mic appears to be an adequate predictor for the variation in microbial respiration rate with soil depth, with 95% of variation in normalized respiration rate accounted for by a linear relationship.     

Aerobic Methanotrophic Communities in the Bottom Sediments of Lake Baikal

The results of the first systematical investigation into the aerobic methanotrophic communities inhabiting the bottom sediments of Lake Baikal have been reported. Use of the radioisotopic method revealed methane consumption in 12 10- to 50-cm-long sediment cores. The maximum methane consumption rates (495–737 µl/(dm³ day) were recorded in sediments in the regions of hydrothermal vents and oil and gas occurrence. Methane consumption was most active in the surface layers of the sediments (0–4 cm); it decreased with the sediment depth and became negligible or absent at depths below 20 cm. The number of methanotrophic bacteria usually ranged from 100 to 1000 cells/cm³ of sediment and reached 1 million cells/cm³ in the regions of oil and gas occurrence. The seventeen enrichment cultures obtained were represented mainly by morphotype II methanotrophs. Phylogenetic analysis of the enrichment cultures in terms of the amino acid sequence of the α subunit of the membrane-bound methane monooxygenase (MMO) revealed the predominance of methanotrophs of the genus Methylocystis. The results obtained suggest the presence of an active aerobic methanotrophic community in Lake Baikal.__________Translated from Mikrobiologiya, Vol. 74, No. 4, 2005, pp. 562–571.Original Russian Text Copyright © 2005 by Gainutdinova, Eshinimaev, Tsyrenzhapova, Dagurova, Suzina, Khmelenina, Namsaraev, Trotsenko.     

Effect of cadmium on composition and diversity of bacterial communities in activated sludges

Microbial communities of two kinds of activated sludge for removing carbon, nitrogen and phosphate (nutrient removal sludge) were identified and compared by combining cloning–denaturing gradient gel electrophoresis methods. The sludges were sampled in an anaerobic–anoxic–oxic system operating under the same conditions, except for one without the addition of cadmium (Cd0) and the other with addition of 5 mg cadmium l⁻¹ (Cd5). Bacteria in the phylum Proteobacteria were predominant in both Cd0 and Cd5 sludges (39.6% and 35.1% of total bacteria, respectively). However, bacteria in the class Betaproteobacteria were significantly more abundant in Cd0 than in Cd5 sludge (30.7% and 2.1%, respectively). Species related to nutrient removal, such as nitrifying bacteria (Nitrosomonas communis), floc-forming bacteria (Zoogloea ramigera) and phosphate-accumulating organisms (Rubrivivax gelatinosus), were the predominant species in Cd0 sludge, but were not found in Cd5 sludge. Cadmium was significantly toxic to the bacterial community in nutrient removal sludge, especially to the bacteria in the Betaproteobacteria. The comparison of microbial communities between these two kinds of sludge was further discussed in the paper.     

The Phylogenetic Diversity of Aerobic Organotrophic Bacteria from the Dagang High-Temperature Oil Field

The distribution and species diversity of aerobic organotrophic bacteria in the Dagang high-temperature oil field (China), which is exploited with water-flooding, have been studied. Twenty-two strains of the most characteristic thermophilic and mesophilic aerobic organotrophic bacteria have been isolated from the oil stratum. It has been found that, in a laboratory, the mesophilic and thermophilic isolates grow in the temperature, pH, and salinity ranges characteristic of the injection well near-bottom zones or of the oil stratum, respectively, and assimilate a wide range of hydrocarbons, fatty acids, lower alcohols, and crude oil, thus exhibiting adaptation to the environment. Using comparative phylogenetic 16S rRNA analysis, the taxonomic affiliation of the isolates has been established. The aerobic microbial community includes gram-positive bacteria with a high and low G+C content of DNA, and γ and β subclasses of Proteobacteria. The thermophilic bacteria belong to the genera Geobacillus and Thermoactinomyces, and the mesophilic strains belong to the genera Bacillus, Micrococcus, Cellulomonas, Pseudomonas, and Acinetobacter. The microbial community of the oil stratum is dominated by known species of the genus Geobacillus (G. subterraneus, G. stearothermophilus, and G. thermoglucosidasius) and a novel species “Geobacillus jurassicus.” A number of novel thermophilic oil-oxidizing bacilli have been isolated.__________Translated from Mikrobiologiya, Vol. 74, No. 3, 2005, pp. 401–409.Original Russian Text Copyright © 2005 by Nazina, Sokolova, Shestakova, Grigoryan, Mikhailova, Babich, Lysenko, Tourova, Poltaraus, Qingxian Feng, Fangtian Ni, Belyaev.     

The response of soil microorganisms and roots to elevated CO2 and temperature in a terrestrial model ecosystem

We investigate the response of soil microorganisms to atmospheric CO2 and temperature change within model terrestrial ecosystems in the Ecotron. The model communities consisted of four plant species (Cardamine hirsuta, Poa annua, Senecio vulgaris, Spergula arvensis), four herbivorous insect species (two aphids, a leaf-miner, and a whitefly) and their parasitoids, snails, earthworms, woodlice, soil-dwelling Collembola (springtails), nematodes and soil microorganisms (bacteria, fungi, mycorrhizae and Protista). In two successive experiments, the effects of elevated temperature (ambient plus 2 °C) at both ambient and elevated CO2 conditions (ambient plus 200 ppm) were investigated. A 40:60 sand:Surrey loam mixture with relatively low nutrient levels was used. Each experiment ran for 9 months and soil microbial biomass (Cmic and Nmic), soil microbial community (fungal and bacterial phospholipid fatty acids), basal respiration, and enzymes involved in the carbon cycling (xylanase, trehalase) were measured at depths of 0–2, 0–10 and 10–20 cm. In addition, root biomass and tissue C:N ratio were determined to provide information on the amount and quality of substrates for microbial growth.Elevated temperature under both ambient and elevated CO2 did not show consistent treatment effects. Elevation of air temperature at ambient CO2 induced an increase in Cmic of the 0–10 cm layer, while at elevated CO2 total phospholipid fatty acids (PLFA) increased after the third generation. The metabolic quotient qCO2 decreased at elevated temperature in the ambient CO2 run. Xylanase and trehalase showed no changes in both runs. Root biomass and C:N ratio were not influenced by elevated temperature in ambient CO2. In elevated CO2, however, elevated temperature reduced root biomass in the 0–10 cm and 30–40 cm layers and increased N content of roots in the deeper layers. The different response of root biomass and C:N ratio to elevated temperature may be caused by differences in the dynamics of root decomposition and/or in allocation patterns to coarse or fine roots (i.e. storage vs. resource capture functions). Overall, our data suggests that in soils of low nutrient availability, the effects of climate change on the soil microbial community and processes are likely to be minimal and largely unpredicatable.     

Diversity,Distribution and Hydrocarbon Biodegradation Capabilities of Microbial Communities in Oil-Contaminated Cyanobacterial Mats from a Constructed Wetland

Various types of cyanobacterial mats were predominant in a wetland, constructed for the remediation of oil-polluted residual waters from an oil field in the desert of the south-eastern Arabian Peninsula, although such mats were rarely found in other wetland systems. There is scarce information on the bacterial diversity, spatial distribution and oil-biodegradation capabilities of freshwater wetland oil-polluted mats. Microbial community analysis by Automated Ribosomal Spacer Analysis (ARISA) showed that the different mats hosted distinct microbial communities. Average numbers of operational taxonomic units (OTUs_ARISA) were relatively lower in the mats with higher oil levels and the number of shared OTUs_ARISA between the mats was <60% in most cases. Multivariate analyses of fingerprinting profiles indicated that the bacterial communities in the wetland mats were influenced by oil and ammonia levels, but to a lesser extent by plant density. In addition to oil and ammonia, redundancy analysis (RDA) showed also a significant contribution of temperature, dissolved oxygen and sulfate concentration to the variations of the mats’ microbial communities. Pyrosequencing yielded 282,706 reads with >90% of the sequences affiliated to Proteobacteria (41% of total sequences), Cyanobacteria (31%), Bacteriodetes (11.5%), Planctomycetes (7%) and Chloroflexi (3%). Known autotrophic (e.g. Rivularia) and heterotrophic (e.g. Azospira) nitrogen-fixing bacteria as well as purple sulfur and non-sulfur bacteria were frequently encountered in all mats. On the other hand, sequences of known sulfate-reducing bacteria (SRBs) were rarely found, indicating that SRBs in the wetland mats probably belong to yet-undescribed novel species. The wetland mats were able to degrade 53–100% of C₁₂–C₃₀ alkanes after 6 weeks of incubation under aerobic conditions. We conclude that oil and ammonia concentrations are the major key players in determining the spatial distribution of the wetland mats’ microbial communities and that these mats contribute directly to the removal of hydrocarbons from oil field wastewaters.     

The Phototrophic Community Found in Lake Khilganta (an Alkaline Saline Lake Located in the Southeastern Transbaikal Region)

The structure of the phototrophic community found in Lake Khilganta (the Agin-Buryat Autonomous Area), a shallow saline soda lake (depth, 35–45 cm; water mineralization, 45 g/l; alkalinity, 30 mg-equiv/l; pH 9.5) has been studied. The bottom of the lake is covered with a 10- to 15-mm microbial mat, whose basis is formed by the filamentous cyanobacterium Microcoleus chthonoplastes. The mat exhibits pronounced layering and contains a significant amount of minerals. Six zones, which have characteristic colors and consistencies and are composed of intermittent layers, have been identified along the vertical profile. Live phototrophic bacteria have been found in the three upper zones. The bulk of the cyanobacteria is concentrated in the upper zone. In the lower zones, the development of purple bacteria has been observed. The diurnal dynamics of the vertical distribution of phototrophic microorganisms, which results from variations in the physicochemical environmental parameters, is described. Ectothiorhodospira sp. are dominant among the anoxyphotobacteria present. Their number, determined according to the inoculation method, is 10⁶–10⁷ cells/ml. The purple bacteria of the genera Allochromatium, Thiocapsa, and Rhodovulum are also present. Experiments with isolated pure cultures have shown that the anoxygenic photosynthetic bacteria of Lake Khilganta are halotolerant and alkalitolerant or alkaliphilic. In liquid enrichment cultures, at pH 9.5, the ratio of anoxyphotobacteria species is close to that observed in the lake. When the pH is increased to 10.4, it is Ectothiorhodospira, which is the most adapted to life under increased mineralization and alkalinity, that predominantly develops. Photosynthetic activity has been observed in the three upper mat zones and constitutes, on average, 1.5 g C/(m²h); the share of anoxygenic photosynthesis accounts for 75–95% of the total productivity. The main role in sulfide oxidation belongs to the phototrophic anoxyphotobacteria and cyanobacteria. In terms of the physicochemical conditions and structure of the phototrophic community, Lake Khilganta is similar to shallow saline water bodies of marine origin. The main differences consist in the increased alkalinity and in the consequent prevalence of alkaliphilic and alkalitolerant microorganisms and in the absence of representatives of the neutrophilic group of green sulfur bacteria.__________Translated from Mikrobiologiya, Vol. 74, No. 3, 2005, pp. 410–419.Original Russian Text Copyright © 2005 by Kompantseva, Sorokin, Gorlenko, Namsaraev.     

Soil-covered strategy for ecological restoration alters the bacterial community structure and predictive energy metabolic functions in mine tailings profiles

Native soil amendment has been widely used to stabilize mine tailings and speed up the development of soil biogeochemical functions before revegetation; however, it remains poorly understood about the response of microbial communities to ecological restoration of mine tailings with soil-covered strategy. In this study, microbial communities along a 60-cm profile were investigated in mine tailings during ecological restoration of two revegetation strategies (directly revegetation and native soil covered) with different plant species. The mine tailings were covered by native soils as thick as 40 cm for more than 10 years, and the total nitrogen, total organic carbon, water content, and heavy metal (Fe, Cu, and Zn) contents in the 0–40 cm intervals of profiles were changed. In addition, increased microbial diversity and changed microbial community structure were also found in the 10–40 cm intervals of profiles in soil-covered area. Soil-covered strategy rather than plant species and soil depth was the main factor influencing the bacterial community, which explained the largest portion (29.96%) of the observed variation. Compared directly to revegetation, soil-covered strategy exhibited the higher relative abundance of Acidobacteria and Deltaproteobacteria and the lower relative abundance of Bacteroidetes, Gemmatimonadetes, Betaproteobacteria, and Gammaproteobacteria. PICRUSt analysis further demonstrated that soil-covered caused energy metabolic functional changes in carbon, nitrogen, and sulfur metabolism. Given all these, the soil-covered strategy may be used to fast-track the establishment of native microbial communities and is conducive to the rehabilitation of biogeochemical processes for establishing native plant species.

     

Links between Geographic Location, Environmental Factors, and Microbial Community Composition in Sediments of the Eastern Mediterranean Sea

The bacterial community composition of marine surface sediments originating from various regions of the Eastern Mediterranean Sea (12 sampling sites) was compared by parallel use of three fingerprinting methods: analysis of 16S rRNA gene fragment heterogeneity by denaturing gradient electrophoresis (DGGE), terminal restriction fragment length polymorphism (T-RFLP), and analysis of phospholipid-linked fatty acid composition (PLFA). Sampling sites were located at variable depths (30–2860 m; water column depth above the sediments) and the sediments differed greatly also in their degree of petroleum contamination (0.4–18 μg g⁻¹), organic carbon (0.38–1.5%), and chlorophyll a content (0.01–7.7 μg g⁻¹). Despite a high degree of correlation between the three different community fingerprint methods, some major differences were observed. DGGE banding patterns showed a significant separation of sediment communities from the northern, more productive waters of the Thermaikos Gulf and the oligotrophic waters of the Cretan, S. Ionian, and Levantine Sea. T-RFLP analysis clearly separated the communities of deep sediments (>1494 m depth) from their shallow (<617 m) counterparts. PLFA analysis grouped a shallow station from the productive waters of the north with the deep oligotrophic sediments from the Ionian and Levantine Sea, with low concentrations of PLFAs, and hence low microbial biomass, as the common denominator. The degree of petroleum contamination was not significantly correlated to the apparent composition of the microbial communities for any of the three methods, whereas organic carbon content and sediment chlorophyll a were important in this regard.