Aerobic methanotrophic communities in the bottom sediments of Lake Baikal

The results of the first methodical investigation into the aerobic methanotrophic communities inhabiting the bottom sediments of Lake Baikal are 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 microl/(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 17 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 alpha subunit of the membrane-bound methane monooxygenase revealed the predominance of methanotrophs of the genus Methylocystis. The results obtained suggest the presence of an active aerobic methanotrophic community in Lake Baikal.     

Diversity of laboratory-reared prokaryotes in the bottom sediments of the Akademichesky Ridge,Lake Baikal

Microbial communities in the bottom sediments of the Akademichesky Ridge, Lake Baikal, were studied. The samples were taken by deep drilling BDP-96 (a 100-m core). Vertical distribution of the prokaryotes with different physiological characteristics was studied for the core. The phylogenetic analysis of the organotrophic laboratory-reared microorganisms revealed the clusterization of Baikal strains and species which have not been identified yet.     

Phylogenetic diversity of microbial communities of the Posolsk Bank bottom sediments,Lake Baikal

Massive parallel sequencing (the Roche 454 platform) of the 16S rRNA gene fragments was used to investigate microbial diversity in the sediments of the Posolsk Bank cold methane seep. Bacterial communities from all sediment horizons were found to contain members of the phyla Actinobacteria, Bacteroidetes, Deinococcus-Thermus, Firmicutes, Nitrospirae, Chloroflexi, Proteobacteria, and the candidate phyla Aminicenantes (OP8) and Atribacteria (OP9). Among Bacteria, members of the Chloroflexi and Proteobacteria were the most numerous (42 and 46%, respectively). Among archaea, the Thaumarchaeota predominated in the upper sediment layer (40.1%), while Bathyarchaeota (54.2%) and Euryarchaeota (95%) were predominant at 70 and 140 cm, respectively. Specific migration pathways of fluid flows circulating in the zone of gas hydrate stability (400 m) may be responsible for considerable numbers of the sequences of Chloroflexi, Acidobacteria, and the candidate phyla Aminicenantes and Atribacteria in the upper sediment layers and of the Deinococcus-Thermus phylum in deep bottom sediments.     

A method for cultivation of microorganisms oxidizing iron and manganese in bottom sediments of Lake Baikal

Methods for cultivation of microorganisms oxidizing iron and manganese in bottom sediments of Lake Baikal were tested. Bacteria were grown on selective media with a characteristic accumulation of metal oxides. The morphology and developmental patterns of the isolated microbial group were studied. The studied sediment core was used to isolate 42 strains of bacteria oxidizing iron and manganese. The cultivated bacteria were confined to the upper sediment layers (down to 11 cm) and their abundance depended on sediment type and redox conditions.     

Isolation of total bacterial DNA for ecological characterization of bottom sediments of Lake Baikal

It is known that the conventional microbiological methods of investigation reveal not more than 1% of the species of microorganisms actually inhabiting one biotope or another. The most complete characterization of the microbial community is achieved by investigating DNA isolated from the samples differing from each other in ecological conditions. The sediments of Lake Baikal are characterized by a high content of humic compounds which hinders molecular biological analyses. Because of this, the procedure of DNA isolation is a step o critical importance for the analysis of bottom sediments. In the present work we compare the methods of isolation of the whole bacterial DNA from the bottom sediments of Lake Baikal. The most efficient method allowing us to obtained DNA preparations for further molecular investigation was chosen.     

Ecophysiological features of mat-forming bacteria Thioploca in bottom sediments of Frolikha Bay, northern Baikal]

A colorless sulfur bacterium of the genus Thioploca, which forms bacterial mats, was studied in the region of underwater thermal vents (Frolikha Bay, northern Baikal). The organism occurs under microaerobic conditions in top sediment layers, and its biomass can amount to 65 mg of wet weight per 1 kg of silt. Individual filaments of the bacterium penetrate the anaerobic zone to the depth of 19 cm. Thioploca is distributed in a mosaic pattern over the bottom of the bay. Thioploca mats are typically found near vents that discharge low-temperature underground water. In the form of separate filaments, this bacterium is more widely distributed in the top sediment layer, particularly in sediments with a more active sulfate reduction. The bacteria from the deep-water and coastal areas of the bay have different morphology. Cells of Thioploca are able to accumulate nitrate, and the coefficient of nitrate accumulation in wet bacterial mass in relation to the near-bottom water is 1.3 x 10(4), suggesting a similarity of metabolism with seawater species. A more lightweight isotopic composition of nitrogen in cell mass as compared to that of representatives of zoobenthos also indicates an active metabolism of nitrogen, apparently, in the process of nitrogen respiration. Comparison of the composition of stable isotopes of carbon in the biomass of representatives of different trophic levels, including Thioploca, found at a depth of 105 m indicates its planktonic origin, whereas, in the deeper bay region, the biomass of Thioploca incorporates more of the light carbon originating from biogenic methane.     

Distribution and chemical fractionation of some heavy metals in bottom sediments of Lake Nasser

Distribution and phase association of Cd, Cr, Cu, Fe, Mn, Ni,Pb, Zn and organic matter in Nile sediments taken from LakeNasser (Aswan, Egypt) were investigated. The sediment sampleswere subjected to selective chemical extraction proceduresdesigned to fractionate the particulate heavy metals into sixfractions: (A) ammonium acetate-extractable metals; (B) sodiumacetate-extractable metals; (C) acid oxalate-extractablemetals; (D) hydroxylamine HCl-extractable metals; (E) aquaregia-extractable metals and (F) total metals (HF/HCl/HNO₃destruction). Exchangeable metals which can be extracted byammonium acetate solution are generally considered readilybioavailable as they are weakly bound and may equilibrateeasily with the aqueous phases. In the present study very smallconcentrations of all heavy metals considered were found inthis phase. Between this phase and the metal phases which arenot bioavailable (those exist in highly resistant phases) thereexist several geochemical phases (fractions B, C & D) that maypotentially release their associated metals under changingenvironmental conditions, such as pH and redox potential in thewater sediment interface. This revised version was published online in July 2006 with corrections to the Cover Date.     

泉州西湖沉积物中硝化细菌的分布及其作用

比较研究泉州西湖沉积物中氨氧化细菌(AOB)和亚硝酸盐氧化细菌(NOB)的分布及氨氧化潜力和亚硝酸盐(NO2?)氧化潜力。结果表明: 西湖沉积物中存在高浓度的有机质(OM)、总氮(TN)和氨氮。AOB生物量为1.1×106?6.4×106 个/g干土, 显著高于NOB生物量4.2×105?7.4×105 个/g 干土(配对t-检验, P<0.05)。对于NOB, 硝化杆菌属(Nitrobacter)和硝化螺菌属(Nitrospira)同时存在于西湖沉积物中, 以Nitrobacter为优势种群。AOB和NOB生物量的差异一定程度上导致西湖沉积物中氨氧化潜力显著高于NO2?氧化潜力(配对t-检验, P<0.05), NO2?氧化过程成为硝化作用的限制步骤。另外, 西湖沉积物中存在的较高浓度氨氮, 一方面促进了AOB的生长和活性, 导致较高速率的氨氧化过程, 另一方面却对亚硝酸盐氧化过程产生选择性抑制, 这也是导致NO2?氧化潜力较低的主要原因之一。     

Bacterial processes of the methane cycle in the bottom sediments of Baikal lake

The activity of methanogenic and methanotrophic bacteria was evaluated in bottom sediments of Lake Baikal. Methane concentration in Baikal bottom sediments varied from 0.0053 to 81.7 ml/dm3. Bacterial methane was produced at rates of 0.0004-534.7 microliters CH4/(dm3 day) and oxidized at rates of 0.005-1180 microliters CH4/(dm3 day). Peak methane production and oxidation were observed in Frolikha Bay near a methane vent. Methane was emitted into water at rates of 49.2-4340 microliters CH4/(m2 day). Rates of bacterial methane oxidation in near-bottom water layers ranged from 0.002 to 1.78 microliters/(1 day). Methanogens and methanotrophs were found to play an important role in the carbon cycle through all layers of sediments, particularly in the areas of methane vent and gas-hydrate occurrence.     

Form and function in manganese-oxidizing bacteria

Summary Stalked, budding bacteria of the genus Hyphomicrobium are shown to be responsible for manganese deposition in freshwater pipelines. The attachment of the cells to the pipe surface is considered from the point of view of electrostatic attraction and the production of holdfast material. Electrophoretic studies indicate that Hyphomicrobium cells are negatively charged and that their surface ionogenic groups are carboxylic. It is postulated that the curious morphology and mode of reproduction of hyphomicrobia accounts for their efficiency in producing, or coexisting with, the manganese oxides they produce.

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Zusammenfassung Die gestielte Bakteriengattung der Hyphomikroben wird für die Manganschlammablagerungen in Süßwasserdruckrohrleitungen verantwortlich gemacht. Die Bindung der Zellen an die Rohroberfläche soll durch elektrostatische Anziehungskraft und Bildung von Haftmaterial bewirkt werden. Die elektrophoretischen Versuche zeigen, daß die Hyphomicrobium-Zellen negativ geladen und die Ionen-Gruppen der Oberfläche Carboxyle sind. Es wird postuliert, daß die eigentümliche Morphologie und Vermehrungsweise der Hyphomikroben verantwortlich sind für ihre Fähigkeit, Manganoxyde zu bilden und mit ihnen gemeinsam zu existieren.

     

红嘴鸥在贝加尔湖的分布和繁殖

在对贝加尔湖地区红嘴鸥Larus ridibundus的数量分布及繁殖习性的现场考察中发现,贝加尔湖及其附近广阔的湿地是红嘴鸥繁殖的理想场所,每年至少有50000对红嘴鸥在当地繁殖;红嘴鸥为半早成鸟;红嘴鸥的筑巢、产卵、孵化是在一定的时间范围内先后不一进行的。这次考察为进一步揭示红嘴鸥的繁殖生态和促进对红嘴鸥及其鸟类的保护提供了一些有益的基础资料。     

The abundance and biological activity of manganese-oxidizing bacteria and Metallogenium-like morphotypes in Lake Washington, USA

The distribution of bacteria, ATP, Metallogenium morphotypes and manganese-oxidizing activities were studied in Lake Washington, Seattle, WA, U.S.A. In accordance with earlier studies, we have found that Metallogenium morphotypes show a stable seasonal distribution in Lake Washington. We have used ⁵⁴Mn(II) tracer studies coupled with poisoned and no-oxygen controls to demonstrate that biological manganese oxidation was not linked to the numbers of Metallogenium morphotypes. The data suggest that these morphotypes do not contribute significantly to the biological oxidation of manganese in Lake Washington.     

Spatial distribution and species composition of prosthecate bacteria in Lake Baikal

From the water column of Lake Baikal, several strains of prosthecate bacteria belonging to the genera Caulobacter and Brevundimonas were isolated. In this article, the methods applied for their isolation and cell number determination are described; the occurrence frequency and spatial distribution of these microorganisms in the lake are demonstrated. Characterization of the species composition of cultivable and uncultivable prosthecate bacteria was carried out using the methods of traditional and molecular microbiology, respectively. A comparative phylogenetic analysis of the DNA sequences of uncultivable bacteria, which showed homology to the members of the alpha subclass of proteobacteria, was carried out. It was demonstrated that the lake water column is inhabited by uncultivable alpha-proteobacteria of uncertain phylogenetic affinity, in addition to representatives of the species Caulobacter vibrioides and C. leidyi, which were detected by traditional microbiological methods.     

Microbial community structure in methane hydrate-bearing sediments of freshwater Lake Baikal

Gas hydrates in marine sediments have been known for many years but recently hydrates were found in the sediments of Lake Baikal, the largest freshwater basin in the world. Marine gas hydrates are associated with complex microbial communities involved in methanogenesis, methane oxidation, sulfate reduction and other biotransformations. However, the contribution of microorganisms to the formation of gas hydrates remains poorly understood. We examined the microbial communities in the hydrate-bearing sediments and water column of Lake Baikal using pyrosequencing of 16S rRNA genes. Aerobic methanotrophic bacteria dominated the water sample collected at the lake floor in the hydrate-bearing site. The shallow sediments were dominated by Archaea. Methanogens of the orders Methanomicrobiales and Methanosarcinales were abundant, whereas representatives of archaeal lineages known to perform anaerobic oxidation of methane, as well as sulfate-reducing bacteria, were not found. Affiliation of archaea to methanogenic rather than methane-oxidizing lineages was supported by analysis of the sequences of the methyl coenzyme M reductase gene. The deeper sediments located at 85-90 cm depth close to the hydrate were dominated by Bacteria, mostly assigned to Chloroflexi, candidate division JS1 and Caldiserica. Overall, our results are consistent with the biological origin of methane hydrates in Lake Baikal.     

Genomic and phenotypic analyses of microorganisms isolated from the sediments of Lake Baikal

Genetic and biochemical methods and morphological examination were used to study microorganisms isolated from samples of deep drilling of the Lake Baikal bottom sediments. Based on blot hybridization patterns, the strains investigated were divided into several groups according to the degree of homology of their genomic DNA. Morphological, biochemical, and ultrastructural characteristics of bacterial strains are described, and their compliance with the genomic analysis data is demonstrated.     

Distribution of dissolved organic carbon in Lake Baikal and its watershed

 Concentrations of dissolved organic carbon (DOC) in Lake Baikal ranged from 90 to 110 μM C, considerably higher than those in oceanic environments. The DOC concentrations in the epilimnion were higher than those in the hypolimnion. Since particulate organic carbon (POC) concentrations in the pelagic waters of Lake Baikal were <10–40 μM C in the epilimnion and 2–5 μM C in the hypolimnion, DOC constitutes a major component of the organic carbon pool in Lake Baikal, especially in the deep layers. The DOC concentrations downstream of the Barguzin and Selenga Rivers were quite high (400–500 μM C). Probably because of the high concentrations of DOC in these rivers, the DOC levels in Barguzin Bay and offshore at the mouth of the Selenga River were higher than those in the pelagic regions of the central and south basins of Lake Baikal. The relationship between DOC and electric conductivity revealed the transport of DOC from rivers to the pelagic area in Lake Baikal. The spatial distribution of DOC suggested that a major part of DOC in the lake was allochthonous (land-derived). Received: July 26, 2002 / Accepted: September 16, 2002 Present address:Research Institute for Humanity and Nature, 335 Takashima-cho, Marutamachi Kawaramachi, Kamigyo-ku, Kyoto 602-0878, Japan Tel. +81-75-229-6167; Fax +81-75-229-6150 e-mail: yos@chikyu.ac.jp Acknowldgments The authors wish to thank Director Prof. M. Grachev and Dr. O. Timoshkin of the Limnological Institute, Siberian Branch, Academy of Science, Russia, for arranging the cruise on Lake Baikal. We are also indebted to Drs. V. Sinyukovich, I. Khanaev, and A. Zhdanov for their kind assistance during the expeditions. We wish to thank Ms. Y. Ito for measuring the DOC concentrations. This work was supported and financed by Grants-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan (No. 09041159) and for Scientific Research of Priority Area B (No. 11213101) and by the International Geosphere-Biosphere Programme (IGBP) at Nagoya University. Correspondence to:T. Yoshioka     

Distribution of zinc-tolerant bacteria in stream sediments

The distribution of zinc-tolerant bacteria in sediments from three stream sites containing high (3125 g g^–1), medium (291 g g^–1), and low (109 g g^–1) concentrations of Zn was determined. Zinc tolerance was estimated by the ability of bacteria to grow on media amended with Zn concentrations ranging from 4 to 512 mg 1^–1. The presence of Zn-tolerant bacteria was correlated with the degree of heavy metal contamination; this correlation was more closely associated with readily extractable heavy metal concentrations than with the more rigorously extracted heavy metals. Low concentrations of Zn in media (4 to 16 mg 1^–1) were stimulatory to growth of bacteria from contaminated sites while concentrations as low as 4 mg 1^–1 were inhibitory to bacteria from the control site.     

Distribution and survival of faecal indicator bacteria in the sediments of the Bay of Vidy,Lake Geneva,Switzerland

The purpose of this study was to determine the concentrations and the horizontal distribution of faecal indicator bacteria (FIB) including Escherichia coli and Enterococcus sp. in the bottom sediments of the Bay of Vidy, City of Lausanne, Switzerland. A vertical distribution of FIB in sediments near the municipal wastewater treatment plant (WWTP) outlet was evaluated and their persistence in those sediments was monitored for a period of 90 days. High FIB levels were measured in the sediments sampled near the WWTP outlet pipe and the mouth of the Chamberonne River, at concentrations ranging between 10⁵ and 10⁷ CFU 100 g^?1. FIB levels at 10 cm depth in the sediments near the WWTP outlet pipe ranged between 10⁴ and 10⁵ CFU 100 g^?1, and were still detected in the top 6 cm after 90 days. Results of this study indicate that freshwater sediments of the Bay of Vidy constitute a reservoir of faecal indicator bacteria, which can persist in certain areas of the bay. Possible resuspension of FIB and pathogens may affect water quality and may increase health risks to sensitive populations during recreational activities. FIB survival in sediments for long periods is of considerable significance for the understanding of microbial pollution in water and for the management of risk at specific recreational coastal sites.