Distance-Decay and Taxa-Area Relationships for Bacteria,Archaea and Methanogenic Archaea in a Tropical Lake Sediment

The study of of the distribution of microorganisms through space (and time) allows evaluation of biogeographic patterns, like the species-area index (z). Due to their high dispersal ability, high reproduction rates and low rates of extinction microorganisms tend to be widely distributed, and they are thought to be virtually cosmopolitan and selected primarily by environmental factors. Recent studies have shown that, despite these characteristics, microorganisms may behave like larger organisms and exhibit geographical distribution. In this study, we searched patterns of spatial diversity distribution of bacteria and archaea in a contiguous environment. We collected 26 samples of a lake sediment, distributed in a nested grid, with distances between samples ranging from 0.01 m to 1000 m. The samples were analyzed using T-RFLP (Terminal restriction fragment length polymorphism) targeting mcrA (coding for a subunit of methyl-coenzyme M reductase) and the genes of Archaeal and Bacterial 16S rRNA. From the qualitative and quantitative results (relative abundance of operational taxonomic units) we calculated the similarity index for each pair to evaluate the taxa-area and distance decay relationship slopes by linear regression. All results were significant, with mcrA genes showing the highest slope, followed by Archaeal and Bacterial 16S rRNA genes. We showed that the microorganisms of a methanogenic community, that is active in a contiguous environment, display spatial distribution and a taxa-area relationship.     

Distribution of Methanogenic and Sulfate-Reducing Bacteria in Near-Shore Marine Sediments

The distribution of methanogenic and sulfate-reducing bacteria was examined in sediments from three sites off the coast of eastern Connecticut and five sites in Long Island Sound. Both bacterial groups were detected at all sites. Three distributional patterns were observed: (i) four sites exhibited methanogenic and sulfate-reducing populations which were restricted to the upper 10 to 20 cm, with a predominance of sulfate reducers; (ii) three sites in western Long Island Sound exhibited a methanogenic population most abundant in sediments deeper than those occupied by sulfate reducers; (iii) at one site that was influenced by fresh groundwater, methanogens and sulfate reducers were numerous within the same depths; however, the number of sulfate reducers varied vertically and temporally with sulfate concentrations. It was concluded that the distributions of abundant methanogenic and sulfate-reducing bacteria were mutually exclusive. Methanogenic enrichments yielded all genera of methanogens except Methanosarcina, with the methanobacteria predominating.     

Anaerobic Ammonia-Oxidizing Bacteria and Related Activity in Baltimore Inner Harbor Sediment

The discovery of bacteria capable of anaerobic ammonia oxidation (anammox) has generated interest in understanding the activity, diversity, and distribution of these bacteria in the environment. In this study anammox activity in sediment samples obtained from the Inner Harbor of Baltimore, Md., was detected by ¹⁵N tracer assays. Anammox-specific oligonucleotide primer sets were used to screen a Planctomycetales-specific 16S rRNA gene library generated from sediment DNA preparations, and four new anammox bacterial sequences were identified. Three of these sequences form a cohesive new branch of the anammox group, and the fourth sequence branches separately from this group. Denaturing gradient gel electrophoresis analysis of sediment incubated with anammox-specific media confirmed the presence of the four anammox-related 16S rRNA gene sequences. Evidence for the presence of anammox bacteria in Inner Harbor sediment was also obtained by using an anammox-specific probe in fluorescence in situ hybridization studies. To our knowledge, this is the first report of anammox activity and related bacterial 16S rRNA gene sequences from the Chesapeake Bay basin area, and the results suggest that this pathway plays an important role in the nitrogen cycle of this estuarine environment. Furthermore, the presence of these bacteria and their activity in sediment strengthen the contention that anammox-related Plactomycetales are globally distributed.     

Distribution of Heterotrophic Bacteria in Lake Shira

A study of the horizontal and vertical distribution of heterotrophic bacteria in brackish Lake Shira in summer periods showed that mesophilic bacteria dominated in all areas of the lake, whereas psychrotolerant bacteria dominated in the metalimnion and hypolimnion of its central part. Nonhalophilic bacteria were mostly mesophilic and dominated in coastal waters. Most psychrotolerant bacteria were able to grow in the presence of 5–10% NaCl. Heterotrophic bacteria isolated in different regions of the lake were identified to a generic level. The isolates were classified into autochthonous and allochthonous microorganisms on the bases of their distribution pattern in the lake water, halotolerance, and ability to grow at low temperatures.     

Distribution of Sulfate-Reducing and Methanogenic Bacteria in Anaerobic Aggregates Determined by Microsensor and Molecular Analyses

Using molecular techniques and microsensors for H₂S and CH₄, we studied the population structure of and the activity distribution in anaerobic aggregates. The aggregates originated from three different types of reactors: a methanogenic reactor, a methanogenic-sulfidogenic reactor, and a sulfidogenic reactor. Microsensor measurements in methanogenic-sulfidogenic aggregates revealed that the activity of sulfate-reducing bacteria (2 to 3 mmol of S²⁻ m⁻³ s⁻¹ or 2 × 10⁻⁹ mmol s⁻¹ per aggregate) was located in a surface layer of 50 to 100 μm thick. The sulfidogenic aggregates contained a wider sulfate-reducing zone (the first 200 to 300 μm from the aggregate surface) with a higher activity (1 to 6 mmol of S²⁻ m⁻³ s⁻¹ or 7 × 10⁻⁹ mol s⁻¹ per aggregate). The methanogenic aggregates did not show significant sulfate-reducing activity. Methanogenic activity in the methanogenic-sulfidogenic aggregates (1 to 2 mmol of CH₄ m⁻³ s⁻¹ or 10⁻⁹ mmol s⁻¹ per aggregate) and the methanogenic aggregates (2 to 4 mmol of CH₄ m⁻³ s⁻¹ or 5 × 10⁻⁹ mmol s⁻¹ per aggregate) was located more inward, starting at ca. 100 μm from the aggregate surface. The methanogenic activity was not affected by 10 mM sulfate during a 1-day incubation. The sulfidogenic and methanogenic activities were independent of the type of electron donor (acetate, propionate, ethanol, or H₂), but the substrates were metabolized in different zones. The localization of the populations corresponded to the microsensor data. A distinct layered structure was found in the methanogenic-sulfidogenic aggregates, with sulfate-reducing bacteria in the outer 50 to 100 μm, methanogens in the inner part, and Eubacteria spp. (partly syntrophic bacteria) filling the gap between sulfate-reducing and methanogenic bacteria. In methanogenic aggregates, few sulfate-reducing bacteria were detected, while methanogens were found in the core. In the sulfidogenic aggregates, sulfate-reducing bacteria were present in the outer 300 μm, and methanogens were distributed over the inner part in clusters with syntrophic bacteria.     

Methanogenic Pathway and Archaeal Community Structure in the Sediment of Eutrophic Lake Dagow: Effect of Temperature

Methanogenic degradation of organic matter is an important microbial process in lake sediments. Temperature may affect not only the rate but also the pathway of CH₄ production by changing the activity and the abundance of individual microorganisms. Therefore, we studied the function and structure of a methanogenic community in anoxic sediment of Lake Dagow, a eutrophic lake in north-eastern Germany. Incubation of sediment samples (in situ 7.5°C) at increasing temperatures (4, 10, 15, 25, 30°C) resulted in increasing production rates of CH₄ and CO₂ and in increasing steady-state concentrations of H₂. Thermodynamic conditions for H₂/CO₂ -dependent methanogenesis were only exergonic at 25 and 30°C. Inhibition of methanogenesis with chloroform resulted in the accumulation of methanogenic precursors, i.e., acetate, propionate, and isobutyrate. Mass balance calculations indicated that less CH₄ was formed via H₂ at 4°C than at 30°C. Conversion of ¹⁴CO₂ to ¹⁴CH₄ also showed that H₂/CO₂ -dependent methanogenesis contributed less to total CH₄ production at 4°C than at 30°C. [2–¹⁴ C]Acetate turnover rates at 4°C accounted for a higher percentage of total CH₄ production than at 30°C. Collectively, these results showed a higher contribution of H₂-dependent methanogenesis and a lower contribution of acetate-dependent methanogenesis at high versus low temperature. The archaeal community was characterized by cloning, sequencing, and phylogenetic analysis of the 16S rRNA genes retrieved from the sediment. Sequences were affiliated with Methanosaetaceae, Methanomicrobiaceae, and three deeply branching euryarchaeotal clusters, i.e., group III, Rice cluster V, and a novel euryarchaeotal cluster, the LDS cluster. Terminal restriction fragment length polymorphism (T-RFLP) analysis showed that 16S rRNA genes affiliated to Methanosaetaceae (20–30%), Methanomicrobiaceae (35–55%), and group III (10–25%) contributed most to the archaeal community. Incubation of the sediment at different temperatures (4–30°C) did not result in a systematic change of the archaeal community composition, indicating that change of temperature primarily affected the activity rather than the structure of the methanogenic community.     

Survival and Activity of Bacteria in a Deep,Aged Lake Sediment (Lake Constance)

Abstract Viable counts and potential activities of different bacteria were determined as a function of depth in the deep profundal sediment of Lake Constance, Germany. The sediment layer at the bottom of the lake had a total depth of about 7 m and was deposited in the time after the last ice age, i.e., over the past 13,000 years. The high clay content of the sediment prevents seepage. Below 25 cm all of the viable heterotrophic bacteria were present as heat-resistant spores. Numbers of viable spores of both aerobic and anaerobic heterotrophic bacteria decreased exponentially with sediment depth and were below the detection limit (5–55 cells ml⁻¹) at 4–6 m, i.e., in about 8,900-year-old sediment. Absence of viable heterotrophic bacteria in deeper sediment layers demonstrated that aseptic sampling conditions were achieved. The decrease of viable spores with depth may be interpreted as time-dependent death of spores resulting in a death rate of about 0.0013–0.0025 year⁻¹. Viable units of specific metabolic groups of bacteria were detected only in the upper sediment layers (0–50 cm). Nitrifying bacteria could not be detected below 30 cm. Methane-oxidizing bacteria were present in the sediment down to >30 cm, but were in a dormant state. Nitrate reduction activity decreased by a factor of 6 within the upper 25 cm of the sediment, but was still detected at 50 cm. Sulfate reduction, on the other hand, could not be detected at depths of 20 cm and below. By contrast, methanogenesis and methanogenic bacteria could be detected down to 50 cm. These observations indicate that bacteria eventually become nonviable in aged sediments. Received: 5 March 1996; Accepted: 12 March 1996     

Vertical Distribution of Bacteria and Algae in a Tropical Lake

In another paper (SCHMIDT, 1969b) the relations between the numbers of bacteria and phytoplankton in the surface layers of some waters near Manaus (Amazonas) were reported. As a stratification of phytoplankton is not possible, due to the strong turbulence in the Rio Solimões (Amazon River), and since current was also present in the Rio Negro off the bays and littoral regions, the vertical distribution of bacteria and algae was of special interest in the Lago do Castanho, the third of the waterbodies investigated in the paper mentioned above. In the present study, two important fractions of bacteria, their total number, and the fraction of saprophyta (estimated by the number of bacterial colonies), were also differentiated.     

Gas Metabolism Evidence in Support of the Juxtaposition of Hydrogen-Producing and Methanogenic Bacteria in Sewage Sludge and Lake Sediments

We developed new techniques to measure dissolved H₂ and H₂ consumption kinetics in anoxic ecosystems that were not dependent on headspace measurements or gas transfer-limited experimentation. These H₂ metabolism parameters were then compared with measured methane production rates, and estimates of H₂ production and interspecies H₂ transfer were made. The H₂ pool sizes were 205 and 31 nM in sewage sludge from an anaerobic digestor and in sediments (24 m) from Lake Mendota, respectively. The H₂ turnover rate constants, as determined by using in situ pool sizes and temperatures, were 103 and 31 h⁻¹ for sludge and sediment, respectively. The observed H₂ turnover rate accounted for only 5 to 6% of the expected H₂-CO₂-dependent methanogenesis in these ecosystems. Our results are in general agreement with the results reported previously and are used to support the conclusion that most of the H₂-dependent methanogenesis in these ecosystems occurs as a consequence of direct interspecies H₂ transfer between juxtapositioned microbial associations within flocs or consortia.     

Microbiological examination of Lake Erie and Lake Ontario sediments

Diver collected cores from three sites in Lake Erie, west of Cleveland, Eastern basin and near Buffalo, and one from Lake Ontario near the mouth of the Niagara River, were sectioned to 20 cm and examined for sulfur cycle and nitrogen cycle bacteria, heterotrophic bacteria, insoluble organic and inorganic phosphate solubilizing bacteria and manganese oxidizing bacteria. Eh, pH, nitrogen, organic carbon and percentage moisture determinations were also made. Data from this study support and confirm other microbiological data collected from Lower Great Lakes sediment and also support the hypothesis that microbial flora of similar type sediments are numerically similar irrespective of the sediments source within the Lower Great Lakes.     

Marine Sediment Bacteria Harbor Antibiotic Resistance Genes Highly Similar to Those Found in Human Pathogens

The ocean is a natural habitat for antibiotic-producing bacteria, and marine aquaculture introduces antibiotics into the ocean to treat infections and improve aquaculture production. Studies have shown that the ocean is an important reservoir of antibiotic resistance genes. However, there is a lack of understanding and knowledge about the clinical importance of the ocean resistome. We investigated the relationship between the ocean bacterial resistome and pathogenic resistome. We applied high-throughput sequencing and metagenomic analyses to explore the resistance genes in bacterial plasmids from marine sediments. Numerous putative resistance determinants were detected among the resistance genes in the sediment bacteria. We also found that several contigs shared high identity with transposons or plasmids from human pathogens, indicating that the sediment bacteria recently contributed or acquired resistance genes from pathogens. Marine sediment bacteria could play an important role in the global exchange of antibiotic resistance.     

Levels of Water-Soluble Vitamins in Methanogenic and Non-Methanogenic Bacteria

The levels of seven water-soluble vitamins in Methanobacterium thermoautotrophicum, Methanococcus voltae, Escherichia coli, Bacillus subtilis, Pseudomonas fluorescens, and Bacteroides thetaiotaomicron were compared by using a vitamin-requiring Leuconostoc strain. Both methanogens contained levels of folic acid and pantothenic acid which were approximately two orders of magnitude lower than levels in the nonmethanogens. Methanobacterium thermoautotrophicum contained levels of thiamine, biotin, nicotinic acid, and pyridoxine which were approximately one order of magnitude lower than levels in the nonmethanogens. The thiamine level in Methanococcus voltae was approximately one order of magnitude lower than levels in the nonmethanogens. Only the levels of riboflavin (and nicotinic acid and pyridoxine in Methanococcus voltae) were approximately equal in the methanogens and nonmethanogens. Folic acid may have been present in extracts of methanogens merely as a precursor, by-product, or hydrolysis product of methanopterin.     

Molecular Identification of Aeromonas and Coliform Bacteria Isolated on m Endo Media from Lake Erie Waters

Summary Bacteria from recreational waters collected from two Lake Erie beaches in Dunkirk, New York were plated onto m Endo LES media. The 16S rRNA gene was then amplified from coliform and non-coliform bacteria using the polymerase chain reaction. The PCR products were characterized by restriction fragment length polymorphism (RFLP) analysis. A total of 8 RFLP groups were identified from the analysis of 920 samples and selected PCR products from each group were sequenced. The DNA sequence analysis indicated that more than half of the bacteria identified as coliforms on the m Endo plates belonged to the genus Aeromonas from the family Aeromonadaceae. Most of the remaining coliforms were from the Enterobacteriaceae. The data indicate that m Endo agar plates allow the growth of non-coliform bacteria, especially Aeromonas species.     

Distribution of Methylomonas methanica and Methylosinus trichosporium in Cleveland Harbor as Determined by an Indirect Fluorescent Antibody-Membrane Filter Technique

An indirect fluorescent antibody-membrane filter staining technique, which permitted the autecological study of Methylomonas methanica and Methylosinus trichosporium, was developed. This technique was used to assay the numbers of these two organisms in Cleveland Harbor. The concentrations of M. methanica and M. trichosporium were found to be inversely proportional to the sampling depth, with the highest cell counts observed in the sediments. M. methanica was observed at every sampling station, whereas M. trichosporium was found at only two of the stations.     

Metabolic Pathways in Methanococcus jannaschii and Other Methanogenic Bacteria

Eleven strains of methanogenic bacteria were divided into two groups on the basis of the directionality (oxidative or reductive) of their citric acid pathways. These pathways were readily identified for most methanogens from the patterns of carbon atom labeling in glutamate, following growth in the presence of [2-¹³C]acetate. All used noncyclic pathways, but members of the family Methanosarcinaceae were the only methanogens found to use the oxidative direction. Methanococcus jannaschii failed to incorporate carbon from acetate despite transmembrane equilibration comparable to other weak acids. This organism was devoid of detectable activities of the acetate-incorporating enzymes acetyl coenzyme A synthetase, acetate kinase, and phosphotransacetylase. However, incorporation of [1-¹³C]-, [2-¹³C]-, or [3-¹³C]pyruvate during the growth of M. jannaschii was possible and resulted in labeling patterns indicative of a noncyclic citric acid pathway operating in the reductive direction to synthesize amino acids. Carbohydrates were labeled consistent with glucogenesis from pyruvate. Leucine, isoleucine, phenylalanine, lysine, formate, glycerol, and mevalonate were incorporated when supplied to the growth medium. Lysine was preferentially incorporated into the lipid fraction, suggesting a role as a phytanyl chain precursor.     

Minimum Threshold for Hydrogen Metabolism in Methanogenic Bacteria

Methanogenic isolates did not consume hydrogen below partial pressures of 6.5 Pa. Thus, in contrast to a previous report, results from pure-culture studies do not invalidate the threshold model for methane production from hydrogen in sediments.     

一种产甲烷优势菌群的筛选方法

目的:用简便易行的产甲烷优势菌群的筛选方法,筛选出能够人工培养的且高效产甲烷的复合微生物.方法:用乙酸钠除氧培养基驯化富含产甲烷菌的厌氧活性污泥,逐渐增加驯化体系中培养基和菌液的比率,使驯化体系中微生物菌群适应人工培养条件.结果:筛选出4个产甲烷优势菌群.筛选出的1号、2号、3号、5号菌群在培养7d后均产甲烷量分别达到46mL、38mL、51mL、38mL,在短时间内4个菌群产甲烷量能持续稳定上升.结论:验证表明建立的方法筛选高效产甲烷菌群简便易行,为沼气工作者提供了一定的参考.     

Isolation and Characterization of Methanogenic Bacteria from Landfills

Methanogenic bacteria were isolated from landfill sites in the United Kingdom. Strains of Methanobacterium formicicum, Methanosarcina barkeri, several different immunotypes of Methanobacterium bryantii, and a coccoid methanogen distinct from the reference immunotypes were identified.     

Production and Distribution of the Microphytobenthos in the Sediment of Lake Mikolajskie

Chlorophyll-α concentration, algal biomass and photosynthetic activity decrease with increasing sediment depth. Chlorophyll-α and biomass minima were found at the sediment surface on several occasions. This may be due to the removal of algae by wave action or vertical migrations of the algae in the sediment. By comparing stations with different degrees of exposure it was shown that wave action affects the size of the benthic populations. The epipsammic microphytobenthos is an important primary producer in the littoral zone of Lake Mikolajskie.