Seasonal and spatial community dynamics in the meromictic Lake Cadagno

Genomic insights into the coupling of a Chlorella-like microeukaryote and sulfur bacteria in the chemocline of permanently stratified Lake Cadagno

Meromictic Lake Cadagno is a permanently stratified system with a persistent microbial bloom within the oxic-anoxic boundary called the chemocline. The association between oxygenic and anoxygenic photosynthesis within the chemocline has been known for at least two decades. Although anoxygenic purple and green sulfur bacteria have been well studied, reports on oxygenic phytoplankton have remained sparse since their discovery in the 1920s. Nearly a century later, this study presents the first near-complete genome of a photosynthetic microbial eukaryote from the chemocline of Lake Cadagno, provisionally named Chlorella-like MAG. The 18.9 Mbp nuclear genome displays a high GC content (71.5%), and the phylogenetic placement suggests that it is a novel species of the genus Chlorella of Chlorophytes. Functional annotation of the Chlorella-like metagenome-assembled genome predicted 10,732 protein-coding genes, with an approximate 0.6% proportion potentially involved in carbon, sulfur, and nitrogen (C, N, and S) metabolism. In addition to C4 photosynthesis, this study detected genes for heat shock proteins (HSPs) in the Chlorella-like algae, consistent with the other Chlorella species. Altogether, the genomic insights in this study suggest the cooperation of photosynthetic algae with phototrophic sulfur bacteria via C, N, and S metabolism, which may aid their collective persistence in the Lake Cadagno chemocline. Furthermore, this work additionally presents the chloroplast genome of Cryptomonas-like species, which was likely to be presumed as cyanobacteria in previous studies because of the presence of phycobilisomes.

Water diversion induces more changes in bacterial and archaeal communities of river sediments than seasonality

Previous studies have demonstrated that seasonal variation is often the most important factor affecting aquatic bacterial assemblages. Whether anthropogenic activities can dominate community dynamics remains unknown. Based on 16S rRNA high-throughput sequencing technology, this study revealed and compared the relative influence of water diversions and seasonality on bacterial and archaeal communities in river sediments from a region with obvious seasonality. The results indicate that the influence of water diversion on bacteria and archaea in water-receiving river sediments exceeded the influence of seasonal variation. Water diversion affected microbes by increasing EC, salinity, water flow rate, and organic matter carbon and nitrogen contents. Seasonal variations affected microbes by altering water temperature. Diversion responders but no season responders were classified by statistical methods in the microbial community. Diversion responder numbers were related to nitrogen concentrations, complex organic carbon contents and EC values, which were mainly affected by water diversion. With the joint impact of water diversion and seasonality, the correlations of bacterial and archaeal numbers with environmental factors were obviously weakened due to the increases in the ecological niche breadths of microorganisms. Natural seasonal changes in bacterial and archaeal communities were totally altered by changes in salinity, nutrients, and hydrological conditions induced by anthropogenic water diversions. These results highlight that human activity may be a stronger driver than natural seasonality in the alteration of bacterial and archaeal communities.

The Microbiome of Size-Fractionated Airborne Particles from the Sahara Region

Diverse airborne microbes affect human health and biodiversity, and the Sahara region of West Africa is a globally important source region for atmospheric dust. We collected size-fractionated (>10, 10-2.5, 2.5-1.0, 1.0-0.5, and <0.5 μm) atmospheric particles in Mali, West Africa and conducted the first cultivation-independent study of airborne microbes in this region using 16S rRNA gene sequencing. Abundant and diverse microbes were detected in all particle size fractions at levels higher than those previously hypothesized for desert regions. Average daily abundance was 1.94 × 10⁵ 16S rRNA copies/m³. Daily patterns in abundance for particles <0.5 μm differed significantly from other size fractions likely because they form mainly in the atmosphere and have limited surface resuspension. Particles >10 μm contained the greatest fraction of daily abundance (51-62%) and had significantly greater diversity than smaller particles. Greater bacterial abundance of particles >2.5 μm that are bigger than the average bacterium suggests that most airborne bacteria are present as aggregates or attached to particles rather than as free-floating cells. Particles >10 μm have very short atmospheric lifetimes and thus tend to have more localized origins. We confirmed the presence of several potential pathogens using polymerase chain reaction that are candidates for viability and strain testing in future studies. These species were detected on all particle sizes tested, including particles <2.5 μm that are expected to undergo long-range transport. Overall, our results suggest that the composition and sources of airborne microbes can be better discriminated by collecting size-fractionated samples.

Draft Genome Sequence of Chromatium okenii Isolated from the Stratified Alpine Lake Cadagno

Blooms of purple sulfur bacteria (PSB) are important drivers of the global sulfur cycling oxidizing reduced sulfur in intertidal flats and stagnant water bodies. Since the discovery of PSB Chromatium okenii in 1838, it has been found that this species is characteristic of for stratified, sulfidic environments worldwide and its autotrophic metabolism has been studied in depth since. We describe here the first high-quality draft genome of a large-celled, phototrophic, γ-proteobacteria of the genus Chromatium isolated from the stratified alpine Lake Cadagno, C. okenii strain LaCa. Long read technology was used to assemble the 3.78 Mb genome that encodes 3,016 protein-coding genes and 67 RNA genes. Our findings are discussed from an ecological perspective related to Lake Cadagno. Moreover, findings of previous studies on the phototrophic and the proposed chemoautotrophic metabolism of C. okenii were confirmed on a genomic level. We additionally compared the C. okenii genome with other genomes of sequenced, phototrophic sulfur bacteria from the same environment. We found that biological functions involved in chemotaxis, movement and S-layer-proteins were enriched in strain LaCa. We describe these features as possible adaptions of strain LaCa to rapidly changing environmental conditions within the chemocline and the protection against phage infection during blooms. The high quality draft genome of C. okenii strain LaCa thereby provides a basis for future functional research on bioconvection and phage infection dynamics of blooming PSB.

Transport-Induced Spatial Patterns of Sulfur Isotopes (δ34S) as Biosignatures

Cave minerals deposited in the presence of microbes may host geochemical biosignatures that can be utilized to detect subsurface life on Earth, Mars, or other habitable worlds. The sulfur isotopic composition of gypsum (CaSO₄·2H₂O) formed in the presence of sulfur-oxidizing microbes in the Frasassi cave system, Italy, was evaluated as a biosignature. Sulfur isotopic compositions (δ³⁴S_V-CDT) of gypsum sampled from cave rooms with sulfidic air varied from -11 to -24‰, with minor deposits of elemental sulfur having δ³⁴S values between -17 and -19‰. Over centimeter-length scales, the δ³⁴S values of gypsum varied by up to 8.5‰. Complementary laboratory experiments showed negligible fractionation during the oxidation of elemental sulfur to sulfate by Acidithiobacillus thiooxidans isolated from the caves. Additionally, gypsum precipitated in the presence and absence of microbes at acidic pH characteristic of the sulfidic cave walls has δ³⁴S values that are on average 1‰ higher than sulfate. We therefore interpret the 8.5‰ variation in cave gypsum δ³⁴S (toward more negative values) to reflect the isotopic effect of microbial sulfide oxidation directly to sulfate or via elemental sulfur intermediate. This range is similar to that expected by abiotic sulfide oxidation with oxygen, thus complicating the use of sulfur isotopes as a biosignature at centimeter-length scales. However, at the cave room (meter-length) scale, reactive transport modeling suggests that the overall ∼13‰ variability in gypsum δ³⁴S reflects isotopic distillation of circulating H₂S gas due to microbial sulfide oxidation occurring along the cave wall-atmosphere interface. Systematic variations of gypsum δ³⁴S along gas flow paths can thus be interpreted as biogenic given that slow, abiotic oxidation cannot produce the same spatial patterns over similar length scales. The expression and preservation potential of this biosignature is dependent on gas flow parameters and diagenetic processes that modify gypsum δ³⁴S values over geological timescales. Key Words: Gypsum-Sulfur isotopes-Biosignature-Sulfide oxidation-Cave. Astrobiology 18, 59-72.

Bacterial abundance and diversity in pond water supplied with different feeds

The abundance and diversity of bacteria in two types of ponds were investigated by quantitative PCR and Illumina MiSeq sequencing. The results revealed that the abundance of bacterial 16S rRNA genes in D ponds (with grass carp fed sudan grass) was significantly lower than that in E ponds (with grass carp fed commercial feed). The microbial communities were dominated by Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria in both E and D ponds, while the abundance of some genera was significantly different between the two types of ponds. Specifically, some potential pathogens such as Acinetobacter and Aeromonas were found to be significantly decreased, while some probiotics such as Comamonadaceae unclassified and Bacillales unclassified were significantly increased in D ponds. In addition, water quality of D ponds was better than that of E ponds. Temperature, dissolved oxygen and nutrients had significant influence on bacterial communities. The differences in bacterial community compositions between the two types of ponds could be partially explained by the different water conditions.

Microbial community diversity, structure and assembly across oxygen gradients in meromictic marine lakes, Palau

Microbial communities consume oxygen, alter biogeochemistry and compress habitat in aquatic ecosystems, yet our understanding of these microbial-biogeochemical-ecological interactions is limited by a lack of systematic analyses of low-oxygen ecosystems. Marine lakes provide an ideal comparative system, as they range from well-mixed holomictic lakes to stratified, anoxic, meromictic lakes that vary in their vertical extent of anoxia. We examined microbial communities inhabiting six marine lakes and one ocean site using pyrosequencing of 16S rRNA genes. Microbial richness and evenness was typically highest in the anoxic monimolimnion of meromictic lakes, with common marine bacteria present in mixolimnion communities replaced by anoxygenic phototrophs, sulfate-reducing bacteria and SAR406 in the monimolimnion. These sharp changes in community structure were linked to environmental gradients (constrained variation in redundancy analysis = 68%-76%) - particularly oxygen and pH. However, in those lakes with the steepest oxygen gradients, salinity and dissolved nutrients were important secondary constraining variables, indicating that subtle but substantive differences in microbial communities occur within similar low-oxygen habitats. Deterministic processes were a dominant influence on whole community assembly (all nearest taxon index values >4), demonstrating that the strong environmental gradients present in meromictic marine lakes drive microbial community assembly.

Stability of bacterial composition and activity in different salinity waters in the dynamic Patos Lagoon estuary: evidence from a lagrangian-like approach

We employed a Lagrangian-like sampling design to evaluate bacterial community composition (BCC--using temporal temperature gel gradient electrophoresis), community-level physiological profiles (CLPP--using the EcoPlate™ assay), and influencing factors in different salinity waters in the highly dynamic Patos Lagoon estuary (southern Brazil) and adjacent coastal zone. Samples were collected monthly by following limnetic-oligohaline (0-1), mesohaline (14-16), and polyhaline (28-31) waters for 1 year. The BCC was specific for each salinity range, whereas the CLPPs were similar for mesohaline and polyhaline waters, and both were different from the limnetic-oligohaline samples. The limnetic-oligohaline waters displayed an oxidation capacity for almost all organic substrates tested, whereas the mesohaline and polyhaline waters presented lower numbers of oxidized substrates, suggesting that potential activities of bacteria increased from the polyhaline to oligohaline waters. However, the polyhaline samples showed a higher utilization of some simple carbohydrates, amino acids, and polymers, indicating a shortage of inorganic nutrients (especially nitrogen) and organic substrates in coastal saltwater. The hypothesis of bacterial nitrogen limitation was corroborated by the higher Nuse index (an EcoPlate™-based nitrogen limitation indicator) in the polyhaline waters and the importance of NO(2)(-), NO(3)(-), low-molecular-weight substances, and the low-molecular-weight:high-molecular-weight substances ratio, indicated by the canonical correspondence analyses (CCAs). Our results demonstrate the important stability of microbial community composition and potential metabolic activity in the different water salinity ranges, which are independent of the region and time of the year of sample collection in the estuary. This is a quite unexpected result for a dynamic environment such as the Patos Lagoon estuary.

Spatio-temporal distribution of phototrophic sulfur bacteria in the chemocline of meromictic Lake Cadagno (Switzerland)

Abstract In situ hybridization was used to study the spatio-temporal distribution of phototrophic sulfur bacteria in the permanent chemocline of meromictic Lake Cadagno, Switzerland. At all four sampling times during the year the numerically most important phototrophic sulfur bacteria in the chemocline were small-celled purple sulfur bacteria of two yet uncultured populations designated D and F. Other small-celled purple sulfur bacteria (Amoebobacter purpureus and Lamprocystis roseopersicina) were found in numbers about one order of magnitude lower. These numbers were similar to those of large-celled purple sulfur bacteria (Chromatium okenii) and green sulfur bacteria that almost entirely consisted of Chlorobium phaeobacteroides. In March and June when low light intensities reached the chemocline, cell densities of all populations, with the exception of L. roseopersicina, were about one order of magnitude lower than in August and October when light intensities were much higher. Most populations were evenly distributed throughout the whole chemocline during March and June, while in August and October a microstratification of populations was detected suggesting specific eco-physiological adaptations of different populations of phototrophic sulfur bacteria to the steep physico-chemical gradients in the chemocline of Lake Cadagno.

Development of a real-time PCR method for the detection of fossil 16S rDNA fragments of phototrophic sulfur bacteria in the sediments of Lake Cadagno

Lake Cadagno is a crenogenic meromictic lake situated in the southern range of the Swiss Alps characterized by a compact chemocline that has been the object of many ecological studies. The population dynamics of phototrophic sulfur bacteria in the chemocline has been monitored since 1994 with molecular methods such as 16S rRNA gene clone library analysis. To reconstruct paleo-microbial community dynamics, we developed a quantitative real-time PCR methodology for specific detection of 16S rRNA gene sequences of purple and green sulfur bacteria populations from sediment samples. We detected fossil 16S rDNA of nine populations of phototrophic sulfur bacteria down to 9-m sediment depth, corresponding to about 9500 years of the lake's biogeological history. These results provide the first evidence for the presence of 16S rDNA of anoxygenic phototrophic bacteria in Holocene sediments of an alpine meromictic lake and indicate that the water column stratification and the bacterial plume were already present in Lake Cadagno thousands of years ago. The finding of Chlorobium clathratiforme remains in all the samples analyzed shows that this population, identified in the water column only in 2001, was already a part of the lake's biota in the past.

Vertical distribution of Archaea and Bacteria in a meromictic lake as determined by fluorescent in situ hybridization

The prokaryotic cells distribution in the water column of the coastal saline meromictic Lake Faro (Messina, Italy) was investigated by microscopic counting techniques. Water samples were collected at a central station from the surface to the bottom, when waters were characterized by a marked stratification. A "red-water" layer, caused by a dense growth of photosynthetic sulfur bacteria, was present at a depth of 15 m, defining a transition area between oxic (mixolimnion) and anoxic (monimolimnion) layers. Fluorescently labeled 16S rRNA oligonucleotide, group-specific probes were used to determine the abundance of Bacteria and Archaea, and their subgroups, Green Sulfur Bacteria (GSB), Sulfate Reducing Bacteria (SRB), Cyanobacteria and Chromatium okenii, and Crenarchaeota and Euryarchaeota, as key elements of the microbial community. Bacteria decreased from surface to bottom, while Archaea increased with depth and reached the maximum value at 30 m, where they outnumbered the Bacteria. Bacteria and picophytoplankton prevailed in the mixolimnion. At the chemocline high numbers of prokaryotic cells were present, mainly represented by Cyanobacteria, Chromatium okenii and Euryarchaeota. GSB, SRB, and Crenarchaeota prevailed below the chemocline. Although Archaea constitute a minor fraction of microbial community, they could represent active contributors to the meromictic Lake Faro ecosystem.

Confirmation of the sequence of 'Candidatus Liberibacter asiaticus' and assessment of microbial diversity in Huanglongbing-infected citrus phloem using a metagenomic approach

The citrus disease Huanglongbing (HLB) is highly destructive in many citrus-growing regions of the world. The putative causal agent of this disease, 'Candidatus Liberibacter asiaticus', is difficult to culture, and Koch's postulates have not yet been fulfilled. As a result, efforts have focused on obtaining the genome sequence of 'Ca. L. asiaticus' in order to give insight on the physiology of this organism. In this work, three next-generation high-throughput sequencing platforms, 454, Solexa, and SOLiD, were used to obtain metagenomic DNA sequences from phloem tissue of Florida citrus trees infected with HLB. A culture-independent, polymerase chain reaction (PCR)-independent analysis of 16S ribosomal RNA sequences showed that the only bacterium present within the phloem metagenome was 'Ca L. asiaticus'. No viral or viroid sequences were identified within the metagenome. By reference assembly, the phloem metagenome contained sequences that provided 26-fold coverage of the 'Ca. L. asiaticus' contigs in GenBank. By the same approach, phloem metagenomic data yielded less than 0.2-fold coverage of five other alphaproteobacterial genomes. Thus, phloem metagenomic DNA provided a PCR-independent means of verifying the presence of 'Ca L. asiaticus' in infected tissue and strongly suggests that no other disease agent was present in phloem. Analysis of these metagenomic data suggest that this approach has a detection limit of one 'Ca. Liberibacter' cell for every 52 phloem cells. The phloem sample sequenced here is estimated to have contained 1.7 'Ca. Liberibacter' cells per phloem cell.

Culture-independent identification of gut bacteria correlated with the onset of diabetes in a rat model

Bacteria associated with the onset of type 1 diabetes in a rat model system were identified. In two experiments, stool samples were collected at three time points after birth from bio-breeding diabetes-prone (BB-DP) and bio-breeding diabetes-resistant (BB-DR) rats. DNA was isolated from these samples and the 16S rRNA gene was amplified using universal primer sets. In the first experiment, bands specific to BB-DP and BB-DR genotypes were identified by automated ribosomal intergenic spacer analysis at the time of diabetes onset in BB-DP. Lactobacillus and Bacteroides strains were identified in the BB-DR- and BB-DP-specific bands, respectively. Sanger sequencing showed that the BB-DP and BB-DR bacterial communities differed significantly but too few reads were available to identify significant differences at the genus or species levels. A second experiment confirmed these results using higher throughput pyrosequencing and quantitative PCR of 16S rRNA with more rats per genotype. An average of 4541 and 3381 16S rRNA bacterial reads were obtained from each of the 10 BB-DR and 10 BB-DP samples collected at time of diabetes onset. Nine genera were more abundant in BB-DP whereas another nine genera were more abundant in BB-DR. Thirteen and eleven species were more abundant in BB-DP and BB-DR, respectively. An average of 23% and 10% of all reads could be classified at the genus and species levels, respectively. Quantitative PCR verified the higher abundance of Lactobacillus and Bifidobacterium in the BB-DR samples. Whether these changes are caused by diabetes or are involved in the development of the disease is unknown.

Spatial heterogeneity of bacterial populations in monomictic Lake Estanya (Huesca, Spain)

Bacterial population changes were investigated in the monomictic Lake Estanya by combining microscopic analysis and two molecular methods involving the amplification of 16S rDNA genes using primers for the domain Bacteria and subsequent restriction fragment length polymorphism (PCR-RFLP) and denaturing gradient gel electrophoresis (PCR-DGGE). Both approaches revealed the vertical distribution of predominant microbial morphotypes and phylotypes in both holomictic and stratified periods, respectively, and showed that variations in structure and composition of bacterial populations are occurring in this lake as a function of depth and time. Through principal component analysis (PCA), these shifts could be related to different physicochemical parameters with temperature, oxygen concentration, and the incident light being of paramount importance as structuring variables. Comparison of RFLP and DGGE profiles by scoring similarities using the Jaccard coefficient and then building a multidimensional scaling map (MDS) showed equivalent results. Both techniques revealed that bacterial populations, present in the whole water column in the holomictic period, showed a high similarity with those located in the deeper part of the lake in the stratified period, evidencing that other factors, both biotic and abiotic, should also be considered as a force driving change in the composition of the bacterial community. Furthermore, DGGE analysis showed that sequences from prominent bands were affiliated to members of four major phyla of the domain Bacteria: Cyanobacteria, Bacteroidetes, Proteobacteria, and Actinobacteria, most of which corresponded to heterotrophic bacterial populations involved in carbon, sulfide, and nitrogen biogeochemical cycles, which were indistinguishable under the light microscope.

Characterization of depth-related microbial communities in lake sediment by denaturing gradient gel electrophoresis of amplified 16S rRNA fragments

The characterization of microbial communities of different depth sediment samples was examined by a culture-independent method and compared with physicochemical parameters, those are organic matter (OM), total nitrogen (TN), total phosphorus (TP), pH and redox potential (Eh). Total genomic DNA was extracted from samples derived from different depths. After they were amplified with the GC-341f/907r primer sets of partial bacterial 16S rRNA genes, the products were separated by denaturing gradient gel electrophoresis (DGGE). The profile of DGGE fingerprints of different depth sediment samples revealed that the community structure remained relatively stable along the entire 45 cm sediment core, however, principal-component analysis of DGGE patterns revealed that at greater sediment depths, successional shifts in community structure were evident. The principle coordinates analysis suggested that the bacterial communities along the sediment core could be separated into two groups, which were located 0--20 cm and 21--45 cm, respectively. The sequencing dominant bands demonstrated that the major phylogenetic groups identified by DGGE belonged to Bacillus, Bacterium, Brevibacillus, Exiguobacterium, gamma-Proteobacterium, Acinetobacter sp. and some uncultured or unidentified bacteria. The results indicated the existence of highly diverse bacterial community in the lake sediment core.

Respiratory succession and community succession of bacterioplankton in seasonally anoxic estuarine waters

Anoxia occurs in bottom waters of stratified estuaries when respiratory consumption of oxygen, primarily by bacteria, outpaces atmospheric and photosynthetic reoxygenation. Once water becomes anoxic, bacterioplankton must change their metabolism to some form of anaerobic respiration. Analysis of redox chemistry in water samples spanning the oxycline of Chesapeake Bay during the summer of 2004 suggested that there was a succession of respiratory metabolism following the loss of oxygen. Bacterial community doubling time, calculated from bacterial abundance (direct counts) and production (anaerobic leucine incorporation), ranged from 0.36 to 0.75 day and was always much shorter than estimates of the time that the bottom water was anoxic (18 to 44 days), indicating that there was adequate time for bacterial community composition to shift in response to changing redox conditions. However, community composition (as determined by PCR-denaturing gradient gel electrophoresis analysis of 16S rRNA genes) in anoxic waters was very similar to that in surface waters in June when nitrate respiration was apparent in the water column and only partially shifted away from the composition of the surface community after nitrate was depleted. Anoxic water communities did not change dramatically until August, when sulfate respiration appeared to dominate. Surface water populations that remained dominant in anoxic waters were Synechococcus sp., Gammaproteobacteria in the SAR86 clade, and Alphaproteobacteria relatives of Pelagibacter ubique, including a putative estuarine-specific Pelagibacter cluster. Populations that developed in anoxic water were most similar (<92% similarity) to uncultivated Firmicutes, uncultivated Bacteroidetes, Gammaproteobacteria in the genus Thioalcalovibrio, and the uncultivated SAR406 cluster. These results indicate that typical estuarine bacterioplankton switch to anaerobic metabolism under anoxic conditions but are ultimately replaced by different organisms under sulfidic conditions.

Archaeal and bacterial community composition of sediment and plankton from a suboxic freshwater pond

We studied the composition of archaeal and bacterial communities present in the sediment and plankton of a shallow suboxic-to-anoxic freshwater pond with high organic matter input, as an example of a kind of inland freshwater system widely distributed in forests of temperate regions. Molecular surveys based on small subunit rRNA genes showed a remarkably high diversity of lineages within the Bacteria, with a total of 18 phyla or candidate divisions being detected, in addition to a few highly divergent phylotypes of unknown affiliation. We identified members of the five subdivisions of the Proteobacteria, as well as Acidobacteria, Verrucomicrobia, Planctomycetes, Bacteroidetes, Chlorobi, Actinobacteria, Firmicutes, Chloroflexi, Gemmatimonadetes, Spirochaetes, Fibrobacteres and the candidate divisions OD1, OP11, TM6, WS1, WS6 and Termite Group 1 ("Endobacteria"). Candidate division OD1 and beta-Proteobacteria were dominant in the environmental libraries of plankton and sediment, respectively. Archaea were also very diverse, but only members of the Euryarchaeota, including Methanosarcinales, Methanomicrobiales and some divergent lineages, were identified. The application of various species richness estimators confirmed the highly diverse nature of both plankton and sediment samples. The pond is a microbial-based complex ecosystem mainly fueled by the degradation of allochthonous organic matter that maintains tightly coupled carbon and sulfur cycles.

The structure and stability of the bacterioplankton community in Antarctic freshwater lakes, subject to extremely rapid environmental change

In this study, variation in the bacterioplankton community structure of three Antarctic lakes of different nutrient status, was determined in relation to physical and chemical gradients at depth and at time intervals, across the seasonal transition from winter ice-cover to the summer ice-free period. The three lakes studied were: Moss Lake (low nutrient, with typical nutrient concentrations of 80 microg l(-1) nitrate and 10 microg l(-1) dissolved reactive phosphate), Sombre Lake (low nutrient, but becoming progressively enriched, with typical nutrient concentrations of 185 microg l(-1) nitrate and 7 microg l(-1) dissolved reactive phosphate) and Heywood Lake (enriched, with typical nutrient concentrations of 1180 microg l(-1) nitrate and 124 microg l(-1) dissolved reactive phosphate). Bacterioplankton community structure was determined using a combination of PCR amplification of 16S rRNA gene fragments and denaturing gradient gel electrophoresis (DGGE). Results indicated marked changes in this bacterioplankton community structure, which were particularly associated with the transition period. However, significant changes also occurred during the period of holomixis. Comparison of the results from lakes of different nutrient status suggest that increased levels of nutrient input, and in the timing and duration of ice cover will lead to marked changes in the structure and stability of the bacterioplankton community at existing levels of environmental change.

An examination of the diversity of a novel Campylobacter reservoir

The diversity of eukaryotic populations, in particular protozoa, in the water supplies of intensively reared broilers has not been previously studied. This important food-rearing environment was screened for the molecular diversity of eukaryotes by the analysis of PCR-amplified 18S rRNA. DNA was extracted from filtered water samples that were collected from the poultry drinking water systems of five farms. The total genomic DNA was used to produce rRNA-PCR amplicons, which, with the application of TTGE, provided an overview of the eukaryotic population diversity. The rRNA-PCR amplicons were then used to generate 34 random clones that were subject to comparative sequence analysis. Twenty-five of the clones (73.5%) showed high similarity with yeasts and fungi (>92%) and 9 clones demonstrated similarity (>86%) with certain protozoan groups, including flagellates and alveolates. Further studies of the microbial diversity in the previously ignored niche of intensively reared poultry drinking water systems are required, along with subsequent in vitro co-culture assays of the detected protozoa and bacterial strains.

Long-term population dynamics of phototrophic sulfur bacteria in the chemocline of Lake Cadagno, Switzerland

Population analyses in water samples obtained from the chemocline of crenogenic, meromictic Lake Cadagno, Switzerland, in October for the years 1994 to 2003 were studied using in situ hybridization with specific probes. During this 10-year period, large shifts in abundance between purple and green sulfur bacteria and among different populations were obtained. Purple sulfur bacteria were the numerically most prominent phototrophic sulfur bacteria in samples obtained from 1994 to 2001, when they represented between 70 and 95% of the phototrophic sulfur bacteria. All populations of purple sulfur bacteria showed large fluctuations in time with populations belonging to the genus Lamprocystis being numerically much more important than those of the genera Chromatium and Thiocystis. Green sulfur bacteria were initially represented by Chlorobium phaeobacteroides but were replaced by Chlorobium clathratiforme by the end of the study. C. clathratiforme was the only green sulfur bacterium detected during the last 2 years of the analysis, when a shift in dominance from purple sulfur bacteria to green sulfur bacteria was observed in the chemocline. At this time, numbers of purple sulfur bacteria had decreased and those of green sulfur bacteria increased by about 1 order of magnitude and C. clathratiforme represented about 95% of the phototrophic sulfur bacteria. This major change in community structure in the chemocline was accompanied by changes in profiles of turbidity and photosynthetically available radiation, as well as for sulfide concentrations and light intensity. Overall, these findings suggest that a disruption of the chemocline in 2000 may have altered environmental niches and populations in subsequent years.

Molecular identification of an uncultured bacterium ("morphotype R") in meromictic Lake Cadagno, Switzerland

Comparative sequence analysis of almost complete 16S rRNA genes of members of the Desulfobacteriaceae retrieved from two gene clone libraries of uncultured bacteria of the chemocline of Lake Cadagno, Switzerland, resulted in the molecular identification of nine sequences, with a tight cluster of five sequences that represented at least three different populations of bacteria with homology values of 95% and 93% to their closest cultured relatives Desulfomonile tiedjei and Desulfomonile limimaris, respectively. In situ hybridization with probes DsmA455 targeting two subpopulations and DsmB455 targeting one subpopulation, detected bacteria with a peculiar morphology previously described as "morphotype R". The individual probes detected about the same number of cells in all samples and together added up to represent all cells of "morphotype R" suggesting that the basic ecophysiological requirements of the subpopulations might be similar. In the monimolimnion, "morphotype R" cells accounted for up to 29% of all Bacteria and entirely represented the Desulfobacteriaceae, the most prominent sulfate-reducing bacteria. In the sediment, "morphotype R" was similarly prominent in the upper cm only where it represented all Desulfobacteriaceae and up to 50% of all Bacteria. Numbers and importance within the Desulfobacteriaceae and Bacteria declined significantly with depth in sediments suggesting potential effects of changing environmental conditions on the fate of "morphotype R".

Geographic and environmental sources of variation in lake bacterial community composition

This study used a genetic fingerprinting technique (automated ribosomal intergenic spacer analysis [ARISA]) to characterize microbial communities from a culture-independent perspective and to identify those environmental factors that influence the diversity of bacterial assemblages in Wisconsin lakes. The relationships between bacterial community composition and 11 environmental variables for a suite of 30 lakes from northern and southern Wisconsin were explored by canonical correspondence analysis (CCA). In addition, the study assessed the influences of ARISA fragment detection threshold (sensitivity) and the quantitative, semiquantitative, and binary (presence-absence) use of ARISA data. It was determined that the sensitivity of ARISA was influential only when presence-absence-transformed data were used. The outcomes of analyses depended somewhat on the data transformation applied to ARISA data, but there were some features common to all of the CCA models. These commonalities indicated that differences in bacterial communities were best explained by regional (i.e., northern versus southern Wisconsin lakes) and landscape level (i.e., seepage lakes versus drainage lakes) factors. ARISA profiles from May samples were consistently different from those collected in other months. In addition, communities varied along gradients of pH and water clarity (Secchi depth) both within and among regions. The results demonstrate that environmental, temporal, regional, and landscape level features interact to determine the makeup of bacterial assemblages in northern temperate lakes.

Vertical and temporal shifts in microbial communities in the water column and sediment of saline meromictic Lake Kaiike (Japan), as determined by a 16S rDNA-based analysis, and related to physicochemical gradients

The vertical and temporal changes in microbial communities were investigated throughout the water column and sediment of the saline meromictic Lake Kaiike by PCR-denaturing gradient gel electrophoresis (DGGE) of 16S rDNA. Marked depth-related changes in microbial communities were observed at the chemocline and the sediment-water interface. However, no major temporal changes in the microbial community below the chemocline were observed during the sampling period, suggesting that the ecosystem in the anoxic zone of Lake Kaiike was nearly stable. Although the sequence of the most conspicuous DGGE band throughout the anoxic water and in the top of the microbial mat was most similar to that of an anoxic, photosynthetic, green sulphur bacterium, Pelodyction luteolum DSM273 (97% similarity), it represented a new phylotype. A comparison of DGGE banding patterns of the water column and sediment samples demonstrated that specific bacteria accumulated on the bottom from the anoxic water layers, and that indigenous microbial populations were present in the sediment. The measurements of bicarbonate assimilation rates showed significant phototrophic assimilation in the chemocline and lithoautotrophic assimilation throughout the anoxic water, but were not clearly linked with net sulphide turnover rates, indicating that sulphur and carbon metabolisms were not directly correlated.

Within- and between-lake variability in the composition of bacterioplankton communities: investigations using multiple spatial scales

This study examined the similarity of epilimnetic bacterial community composition (BCC) across several within- and among-lake spatial scales, and the environmental factors giving rise to similar bacterial communities in different lakes were also explored. Samples were collected from 13 northern and southern Wisconsin lakes representing gradients in lake size, productivity, dissolved organic carbon and humic acid contents, and pH. Hypotheses regarding patchy distribution of bacterial communities in lakes were tested by comparing samples collected from nearby (tens of meters) and distant (hundreds of meters) sampling sites in the same lake. BCC was characterized by using a molecular fingerprinting technique, automated ribosomal intergenic spacer analysis (ARISA). Overall, samples collected at the 10-m, 100-m, and between-lake scales differed by 13, 17, and 75%, respectively. Variation at these last two scales was significant. The development of within-lake variation in BCC appeared to depend on the isolation of water by lake shoreline features such as bays or narrow constrictions. ARISA profiles from northern lakes had fewer peaks and were less similar to each other than were those of the southern lakes, suggesting that regional features do not necessarily lead to the development of similar bacterial communities. Lakes at similar positions on productivity and dissolved organic carbon concentration gradients had similar bacterial communities, and bacterial diversity was positively correlated with lake productivity and water temperature. Factorial studies taking into account these gradients, as well as regional spatial scales, should provide much insight into the nature of aquatic bacterial biogeography.

The identification of microorganisms by fluorescence in situ hybridisation

Fluorescence in situ hybridisation (FISH) with rRNA-targeted oligonucleotide probes facilitates the rapid and specific identification of individual microbial cells in their natural environments. Over the past year there have been a number of methodological developments in this area and new applications of FISH in microbial ecology and biotechnology have been reported.