Microbial biomass and community structure of a phase-separated methanogenic reactor determined by lipid analysis

Summary An anaerobic phase-separation biomass reactor was established on cellulose with the hydrolysis and fermentation steps occurring in the first stage, and acetogenesis and methanogenesis in the second stage. Based upon lipid biomarker analysis, eubacterial and eukaryotic cells accounted for approximately 6% of the volatile solids of the first stage and 17% of the second, while methanogens were approximately 1% of the volatile solids in the first stage and 9% of the second. Clustering the polar lipid fatty acids into groups based upon their distributions between the two stages of the reactor clarified the differences in community structure caused by phase-separated operation. Although inoculated from the same source, the two stages maintained very different microbial communities. Signature fatty acids known as indicators of unbalanced growth in eubacteria were significantly higher in the first stage of the reactor.     

Variation in microbial biomass and community structure in sediments of eutrophic bays as determined by phospholipid ester-linked Fatty acids

[This corrects the article on p. 562 in vol. 58.].     

Water-mass influences on summer Antarctic phytoplankton biomass and community structure

The association between the variability of phytoplankton biomass and community structure and the distribution of water masses around the Antarctic Peninsula were examined during austral summer 1993. Phytoplankton biomass showed high variability, and was dominated by an autotrophic flagellate (Cryptomonas sp.) that represented, on average, 91% of total phytoplankton biomass. The lowest phytoplankton biomasses were associated with the strongly mixed, saline, cold waters characteristic of the Weddell Sea water mass, and with the waters influenced by ice melt from the Bellingshausen Sea. The highest biomasses were found in the confluence of these water masses, where a front develops. Community composition also differed among water masses, with eukariotic picoplankton and diatoms having their highest relative contribution to community biomass in stations with Bellingshausen Sea and Weddell Sea water masses, whereas the abundance of Cryptomonas sp. was highest at the confluence of these waters. These results indicate that mesoscale processes, that determine water mass distribution, are of paramount importance in controlling the time and space variability of Antarctic phytoplankton.     

Microbial community structure and diversity in a native forest wood-decomposed hollow-stump ecosystem

The aim of this study is to investigate the microbial community structure and diversity in a wood-decomposed hollow-stump ecosystem. Microbial communities of SD-1, a lateritic soil sample from forest hollow-stump ecosystems in Fuzhou (a southeastern coast city of China), were characterized by constructing and analyzing rRNA gene clone libraries. Sixty-six phylotypes were identified from 112 bacterial clones, including Acidobacteria (71.5%), Proteobacteria (24.1%) and Verrucomicrobia (0.9%). A total of 40 phylotypes were obtained from 138 fungal clones, including Basidiomycota (42.8%), Ascomycota (36.2%), Zygomycota (13.8%), Chytridiomycota (2.9%) and Fungi incertae sedis (4.3%). The results showed a variety of clones related to the reported lignocellulose-decomposing microorganisms. They included some important bacterial decomposers, such as Sphingomonas and Burkholderia, and a number of wood-decaying fungi, including Tricholomataceae, Strophariaceae and Agaricaceae of Basidiomycota; Orbilia, Aspergillus, Phialocephala, Epicoccum and Phoma of Ascomycota and Mucorales of Zygomycota. The result indicated that the lignocellulolytic microorganisms worked synergically with a unique community structure to biodegrade lignocellulose in the hollow-stump ecosystem.     

Microbial community structure and biomass in developing drinking water biofilms

Traditional techniques to study microbes, such as culturable counts, microbial biomass, or microbial activity, do not give information on the microbial ecology of drinking water systems. The aim of this study was to analyze whether the microbial community structure and biomass differed in biofilms collected from two Finnish drinking water distribution systems (A and B) receiving conventionally treated (coagulation, filtration, disinfection) surface water. Phospholipid fatty acid methyl esters (PLFAs) and lipopolysaccharide 3-hydroxy fatty acid methyl esters (LPS 3-OH-FAs) were analyzed from biofilms as a function of water residence time and development time. The microbial communities were rather stabile through the distribution systems, as water residence time had minor effects on PLFA profiles. In distribution system A, the microbial community structure in biofilms, which had developed in 6 weeks, was more complex than those grown for 23 or 40 weeks. The microbial communities between the studied distribution systems differed, possibly reflecting the differences in raw water, water purification processes, and distribution systems. The viable microbial biomass, estimated on the basis of PLFAs, increased with increasing water residence time in both distribution systems. The quantitative amount of LPS 3-OH-FAs increased with increasing development time of biofilms of distribution system B. In distribution system A, LPS 3-OH-FAs were below the detection limit.     

Microbial community structure in autotrophic nitrifying granules characterized by experimental and simulation analyses

This study evaluates the community structure in nitrifying granules (average diameter of 1600 μm) produced in an aerobic reactor fed with ammonia as the sole energy source by a multivalent approach combining molecular techniques, microelectrode measurements and mathematical modelling. Fluorescence in situ hybridization revealed that ammonia-oxidizing bacteria dominated within the first 200 μm below the granule surface, nitrite-oxidizing bacteria a deeper layer between 200 and 300 μm, while heterotrophic bacteria were present in the core of the nitrifying granule. Presence of these groups also became evident from a 16S rRNA clone library. Microprofiles of NH₄⁺, NO₂^–, NO₃^– and O₂ concentrations measured with microelectrodes showed good agreement with the spatial organization of nitrifying bacteria. One- and two-dimensional numerical biofilm models were constructed to explain the observed granule development as a result of the multiple bacteria–substrate interactions. The interaction between nitrifying and heterotrophic bacteria was evaluated by assuming three types of heterotrophic bacterial growth on soluble microbial products from nitrifying bacteria. The models described well the bacterial distribution obtained by fluorescence in situ hybridization analysis, as well as the measured oxygen, nitrite, nitrate and ammonium concentration profiles. Results of this study are important because they show that a combination of simulation and experimental techniques can better explain the interaction between nitrifying bacteria and heterotrophic bacteria in the granules than individual approaches alone.     

Trophic structure of a coastal fish community determined with diet and stable isotope analyses

A combination of dietary guild analysis and nitrogen (δ¹⁵N) and carbon (δ¹³C) stable‐isotope analysis was used to assess the trophic structure of the fish community in Rhode Island and Block Island Sounds, an area off southern New England identified for offshore wind energy development. In the autumn of 2009, 2010 and 2011, stomach and tissue samples were taken from 20 fish and invertebrate species for analysis of diet composition and δ¹⁵N and δ¹³C signatures. The food chain in Rhode Island and Block Island Sounds comprises approximately four trophic levels within which the fish community is divided into distinct dietary guilds, including planktivores, benthivores, crustacivores and piscivores. Within these guilds, inter‐species isotopic and dietary overlap is high, suggesting that resource partitioning or competitive interactions play a major role in structuring the fish community. Carbon isotopes indicate that most fishes are supported by pelagic phytoplankton, although there is evidence that benthic production also plays a role, particularly for obligate benthivores such as skates Leucoraja spp. This type of analysis is useful for developing an ecosystem‐based approach to management, as it identifies species that act as direct links to basal resources as well as species groups that share trophic roles.     

Stock structure of Lake Baikal omul as determined by whole-body morphology

In Lake Baikal, three morphotypes of omul Coregonus autumnalis migratorius are recognized; the littoral, pelagic, and deep-water forms. Morphotype assignment is difficult, and similar to that encountered in pelagic and deep-water coregonines in the Laurentian Great Lakes. Principal component analysis revealed separation of all three morphotypes based on caudal peduncle length and depth, length and depth of the body between the dorsal and anal fin, and distance between the pectoral and the pelvic fins. Strong negative loadings were associated with head measurements. Omul of the same morphotype captured at different locations were classified to location of capture using step-wise discriminant function analysis. Jackknife correct classifications ranged from 43 to 78% for littoral omul from five locations, and 45–86% for pelagic omul from four locations. Patterns of location misclassification of littoral omul suggested that the sub-population structure, hence stock affinity, may be influenced by movements and intermixing of individuals among areas that are joined bathymetrically. Pelagic omul were more distinguishable by site and may support a previous hypothesis of a spawning-based rather than a foraging-based sub-population structure. Omul morphotypes may reflect adaptations to both ecological and local environmental conditions, and may have a genetic basis.     

Vertical distribution of structure and function of the methanogenic archaeal community in Lake Dagow sediment

Detailed studies on the relation of structure and function of microbial communities in a sediment depth profile scarcely exist. We determined as functional aspect the vertical distribution of the acetotrophic and hydrogenotrophic CH4 production activity by measuring production rates and stable 13C/12C-isotopic signatures of CH4 in the profundal sediment of Lake Dagow. The structural aspect was determined by the composition of the methanogenic community by quantifying the abundance of different archaeal groups using 'real-time' polymerase chain reaction and analysis of terminal restriction fragment length polymorphism (T-RFLP). Methane production rates in the surface sediment (0-3 cm depth) were higher in August than in May, but strongly decreased with depth (down to 20 cm). The delta13C of the produced CH4 and CO2 indicated an increase in isotopic fractionation with sediment depth. The relative contribution of hydrogenotrophic to total methanogenesis, which was calculated from the isotopic signatures, increased with depth from about 22% to 38%. Total numbers of microorganisms were higher in August than in May, but strongly decreased with depth. The increase of microorganisms from May to August mainly resulted from Bacteria. The Archaea, on the other hand, exhibited a rather constant abundance, but also decreased with depth from about 1 x 10(8) copies of the archaeal 16S rRNA gene per gram of dry sediment at the surface to 4 x 10(7) copies per gram at 15-20 cm depth. T-RFLP analysis combined with phylogenetic analysis of cloned sequences of the archaeal 16S rRNA genes showed that the methanogenic community consisted mainly of Methanomicrobiales and Methanosaetaceae. The relative abundance of Methanosaetaceae decreased with depth, whereas that of Methanomicrobiales slightly increased. Hence, the vertical distribution of the functional characteristics (CH4 production from acetate versus H2/CO2) was reflected in the structure of the community consisting of acetotrophic (Methanosaetaceae) versus hydrogenotrophic (Methanomicrobiales) phenotypes.     

The molecular diversity of the methanogenic community in a hypereutrophic freshwater lake determined by PCR-RFLP

AIMS: To combine database-held sequence information with a programme of experimental molecular ecology to define the methanogenic community of a hypereutrophic lake by a PCR-restriction fragment length polymorphism (RFLP) analysis. METHODS AND RESULTS: Methanogen diversity in a hypereutrophic freshwater lake was analysed using 16S rDNA PCR-RFLP. Database-held 16S rRNA gene sequences for 76 diverse methanogens were analysed for specific restriction sites that permitted unequivocal differentiation of methanogens. Restriction digestion and agarose gel electrophoresis of the 16S rDNA from selected methanogen pure cultures generated observed restriction profiles that corroborated the expected patterns. This method was then tested by analysing methanogen diversity in samples obtained over 1 year from sediment and water samples taken from the same sampling site. CONCLUSIONS: Restriction analysis of the 16S rRNA gene sequences from 157 methanogen clones generated from lakewater and sediment samples showed that over 50% were similar to Methanoculleus spp. Furthermore, a total of 16 RFLP types (1-16) were identified, eight of which contained no cultured representative archaeal 16S rRNA gene sequences. SIGNIFICANCE AND IMPACT OF THE STUDY: This RFLP strategy provides a robust and reliable means to rapidly identify methanogens in the environment.     

Bacterial community structure in experimental methanogenic bioreactors and search for pathogenic clostridia as community members

Microbial conversion of organic waste or harvested plant material into biogas has become an attractive technology for energy production. Biogas is produced in reactors under anaerobic conditions by a consortium of microorganisms which commonly include bacteria of the genus Clostridium. Since the genus Clostridium also harbors some highly pathogenic members in its phylogenetic cluster I, there has been some concern that an unintended growth of such pathogens might occur during the fermentation process. Therefore this study aimed to follow how process parameters affect the diversity of Bacteria in general, and the diversity of Clostridium cluster I members in particular. The development of both communities was followed in model biogas reactors from start-up during stable methanogenic conditions. The biogas reactors were run with either cattle or pig manures as substrates, and both were operated at mesophilic and thermophilic conditions. The structural diversity was analyzed independent of cultivation using a PCR-based detection of 16S rRNA genes and genetic profiling by single-strand conformation polymorphism (SSCP). Genetic profiles indicated that both bacterial and clostridial communities evolved in parallel, and the community structures were highly influenced by both substrate and temperature. Sequence analysis of 16S rRNA genes recovered from prominent bands from SSCP profiles representing Clostridia detected no pathogenic species. Thus, this study gave no indication that pathogenic clostridia would be enriched as dominant community members in biogas reactors fed with manure.     

Distribution of sulfate-reducing and methanogenic bacteria in anaerobic aggregates determined by microsensor and molecular analyses.

Using molecular techniques and microsensors for H(2)S and CH(4), 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 S(2-) m(-3) s(-1) or 2 x 10(-9) mmol s(-1) per aggregate) was located in a surface layer of 50 to 100 microm thick. The sulfidogenic aggregates contained a wider sulfate-reducing zone (the first 200 to 300 microm from the aggregate surface) with a higher activity (1 to 6 mmol of S(2-) m(-3) s(-1) or 7 x 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 CH(4) m(-3) s(-1) or 10(-9) mmol s(-1) per aggregate) and the methanogenic aggregates (2 to 4 mmol of CH(4) m(-3) s(-1) or 5 x 10(-9) mmol s(-1) per aggregate) was located more inward, starting at ca. 100 microm 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 H(2)), 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 microm, 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 microm, and methanogens were distributed over the inner part in clusters with syntrophic bacteria.     

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.     

Dynamics of a microbial community associated with manure hot spots as revealed by phospholipid fatty acid analyses.

Microbial community dynamics associated with manure hot spots were studied by using a model system consisting of a gel-stabilized mixture of soil and manure, placed between layers of soil, during a 3-week incubation period. The microbial biomass, measured as the total amount of phospholipid fatty acids (PLFA), had doubled within a 2-mm distance from the soil-manure interface after 3 days. Principal-component analyses demonstrated that this increase was accompanied by reproducible changes in the composition of PLFA, indicating changes in the microbial community structure. The effect of the manure was strongest in the 2-mm-thick soil layer closest to the interface, in which the PLFA composition was statistically significantly different (P < 0.05) from that of the unaffected soil layers throughout the incubation period. An effect was also observed in the soil layer 2 to 4 mm from the interface. The changes in microbial biomass and community structure were mainly attributed to the diffusion of dissolved organic carbon from the manure. During the initial period of microbial growth, PLFA, which were already more abundant in the manure than in the soil, increased in the manure core and in the 2-mm soil layer closest to the interface. After day 3, the PLFA composition of these layers gradually became more similar to that of the soil. The dynamics of individual PLFA suggested that both taxonomic and physiological changes occurred during growth. Examples of the latter were decreases in the ratios of 16:1 omega 7t to 16:1 omega 7c and of cyclopropyl fatty acids to their respective precursors, indicating a more active bacterial community. An inverse relationship between bacterial PLFA and the eucaryotic 20:4 PLFA (arachidonic acid) suggested that grazing was important.     

Soil anammox community structure in different land use soils treatment with 13 C urea as determined by analysis of phospholipid fatty acids

The anaerobic ammonium oxidation (anammox) process is globally an important nitrogen-cycling process mediated by specialized microbes. However, still little information is documented about anammox microbial community structure under agricultural soils. The anaerobic incubation experiment was conducted to study the impacts of different land use soils fertilized by 13C-urea on the activity and diversity of anammox bacteria using stable isotope to probe the phospholipid fatty acid (PLFA-SIP). The 13C was preferentially incorporated in ratios PLFAs 16:1ω7c, 16:1ω5c, and 16:0. The results revealed that the abundance of the anammox bacteria (both hzs-β and hzo) were observed in vegetable soil V1 and paddy soils (R1 and R2) means that they were positively correlated with 13C-urea but were negatively correlated with NO3 −-N and NH4 +-N concentrations. Thus, 13C-PLFAs 16:1ω7c, 16:1ω5c, and 16:0 could be the biomarker as soil anammox. The anaerobic microbial community composition of soils under different land use systems was diverse, and V1, R1, and R2 had similar microbial diversity and higher microbial biomass. The principal component analysis between soil properties and gene abundance suggested that not only pH but also soil organic matter, available P, and available K were important factors for the anammox process. This study suggested that 13C-Urea-PLFA for anaerobic incubation was a simple method to study anammox microbial community structure through affecting the soil nutrients, and the different land use systems played important roles in determining the microbial composition of soils.     

Space use by red deer in a Mediterranean ecosystem as determined by radio-tracking

Space use, movements and activity rhythms of radio-tagged red deer were studied in a Mediterranean environment. The deer were found to be mainly crepuscular, nocturnal activity being higher than diurnal activity, which differs from studies of northern European populations of the species. Home ranges were smaller than most reported in the literature, that of the male being about two or three times larger than those of the females. Daily movements ranged from 3 to 4 km day⁻¹ according to the size of the home range. Vegetation cover was used more by the male and by all individuals during the summer, whilst open areas were used during the winter and spring, probably because of the high grass production in these seasons. The differences found with respect to other populations indicate that further studies in Mediterranean ecosystems are required to provide a basis of knowledge for management decisions.     

东湖沉积物中微生物磷脂的垂向分布

以武汉东湖柱状沉积物为研究对象,利用磷脂法测定了3个采样点各层的微生物量,同时测定了沉积物中各层的pH,简要分析了沉积物中磷脂含量的垂向分布与pH垂向分布的相关性。结果表明:各样点沉积物中磷脂平均含量分别为:1号点59.40nmol/g.dw,2号点为20.56nmol/g.dw,3号点为31.57nmol/g.dw。在沉积物的垂向分布上,微生物量与pH均随着沉积物深度的增加而降低,并且存在很高的相关系数。