Recurring seasonal dynamics of microbial communities in stream habitats

Recurring seasonal patterns of microbial distribution and abundance in three third-order temperate streams within the southeast Pennsylvania Piedmont were observed over 4 years. Populations associated with streambed sediments and rocks (epilithon) were identified using terminal restriction length polymorphism (tRFLP) and sequencing of 16S rRNA genes selectively amplified with primers for the bacterial domain. Analyses of the relative magnitudes of tRFLP peak areas by using nonmetric multidimensional scaling resolved clear seasonal trends in epilithic and sediment populations. Oscillations between two dominant groups of epilithic genotypes, explaining 86% of the seasonal variation in the data set, were correlated with temperature and dissolved organic carbon. Sequences affiliated with epilithic phototrophs (cyanobacteria and diatom chloroplasts), a Rhodoferax sp., and a Bacillus species clustered in the summer, whereas sequences most closely related to Betaproteobacteria (putative Burkholderia sp.), and a putative cyanobacterium clustered in the fall/spring. The sediment genotypes also clustered into two groups, and these explained 85% of seasonal variation but correlated only with temperature. A summer tRFLP pattern was characterized by prevalence of Betaproteobacteria, Gammaproteobacteria, and a Bacillus sp., whereas the winter/spring pattern was characterized by phylotypes most closely related to Firmicutes, Gammaproteobacteria, and Nitrospirae. A close association between these headwater streams and their watersheds was suggested by the recovery of sequences related to microbial populations provisionally attributed to not only freshwaters but also terrestrial habitats.     

Extracellular proteolytic enzymes of microscopic fungi from thermal springs of the Barguzin Valley (Northern Baikal region)

Production of extracellular proteolytic enzymes was studied in thermophilic fungi Paecelomyces variotii and Aspergillus carneus, isolated from thermal springs of the Barguzin Valley. Protease synthesis in these fungi requires protein in the ambient medium. The composition of the enzymes secreted by A. carneus depends on the kind of carbohydrate present in the medium. The proteinase of this fungus digests synthetic substrates and gelatin (optimum pH 7.7). It belongs to neutral serine proteases. Extracellular P. variotii proteases digest gelatin (optimum pH 9.7–10.4). According to inhibitor analysis data, they can be classified as alkaline metalloproteinases and serine proteinases.     

Extracellular proteolytic eyzymes of microscopic fungi from thermal springs of the Barguzin Valley (Northern Baikal region)

Production of extracellular proteolytic enzymes was studied in thermophilic fungi Paecelomyces variotii and Aspergillus carneus, isolated from thermal springs of the Barguzin Valley. Protease synthesis in these fungi requires protein in the ambient medium. The composition of the enzymes secreted by A. carneus depends on the kind of carbohydrate present in the medium. The proteinase of this fungus digests synthetic substrates and gelatin (optimum pH 7.7). It belongs to neutral serine proteases. Extracellular P. variotii proteases digests gelatin (optimum pH 9.7-10.4). According to inhibitor analysis data, they are assigned to alkaline metalloproteinases and serine proteinases.     

Aerobic methanotrophs from the coastal thermal springs of Lake Baikal

The number, activity, and diversity of aerobic methanotrophic bacteria in the sediments of three coastal thermal springs of Lake Baikal were analyzed. The average number of methanotrophs was 10³–10⁴ cells per 1 cm³ of sediment. The highest number of methanotrophs (10⁸ cells/cm³ of silt) and the highest potential rate of methane uptake [7.7 nmol CH₄/(cm³ day)] were revealed in sediments from the Sukhaya thermal spring. The methods of molecular ecology (DGGE, FISH, analysis of pmoA gene fragments) showed the predominance in most enrichment cultures of methanotrophs of type II, i.e., of the genera Methylocystis and Methylosinus. In only one enrichment culture (from the Sukhaya thermal spring), a type I methanotroph was revealed; its similarity to Methylococcus capsulatus Bath did not exceed 80%. These results demonstrate a widespread occurrence and high activity of the aerobic methanotrophic community in the coastal thermal springs of Lake Baikal.     

Taxonomic composition of Lake Baikal bacterioneuston communities

The taxonomic composition of microbial communities of Lake Baikal surface microlayer was studied by pyrosequencing of the 16S rDNA amplicons. Statistically reliable differences were found between bacterioneuston of the shallow and deep-water stations. The shallow station community was characterized by higher diversity than the deep-water one. While bacterioneuston communities were shown to be less diverse than the water column communities, their diversity was comparable to that of other biofilm associations. Microbial communities of Lake Baikal surface microlayer were shown to be similar to those of the water column in the composition of predominant phyla, while differing considerably at the genus level. Bacterioneuston of Lake Baikal was comparable to microbial communities of the surface microlayer of other freshwater basins, although it was characterized by high abundance of the Alphaproteobacteria and Verrucomicrobia. High abundance of photoheterotrophs compared to the water column communities of other freshwater basins was another distinctive feature of Lake Baikal bacterioneuston. Our results showed the Lake Baikal surface microlayer to be a specific microbial community with low species diversity and relatively high abundance of photoheterotrophic microorganisms.     

Phage community dynamics in hot springs

In extreme thermal environments such as hot springs, phages are the only known microbial predators. Here we present the first study of prokaryotic and phage community dynamics in these environments. Phages were abundant in hot springs, reaching concentrations of a million viruses per milliliter. Hot spring phage particles were resistant to shifts to lower temperatures, possibly facilitating DNA transfer out of these extreme environments. The phages were actively produced, with a population turnover time of 1 to 2 days. Phage-mediated microbial mortality was significant, making phage lysis an important component of hot spring microbial food webs. Together, these results show that phages exert an important influence on microbial community structure and energy flow in extreme thermal environments.     

Studies on seasonal dynamics of soil-higher fungal communities in Mongolian oak-dominant Gwangneung forest in Korea

We surveyed macrofungi biweekly at defined plots from April to December in 2014, in the Mongolian oak-dominant forest, Gwangneung Forest, Pochen-si, Korea, and analyzed a soilhigher fungal diversity during four seasons (represented by April, August, October, and December). Based on morphological observation of collected specimens, the collected macrofungi were classified into 2 phyla 3 classes 7 orders, 14 families, 21 genera, and 33 species (36 specimens). DNA-based community analyses indicated that soil-higher fungi were classified into 2 phyla, 18 classes, 49 orders, 101 families, and 155 genera (83,360 sequence reads), defined herein as 155 genus-level operational taxonomic units (GOTUs). In the present study, we evaluated and discussed the fungal diversity in seasonal dynamics and soil layers based on collected macrofungi and pyrosequencing data while considering environmental parameters (pH, exchangeable K, T-P, NH ₄ ⁺ , NO ₃ ^- , OM, WR, TOC, and T-N). Moreover, principal components analysis (PCA) showed distinct clusters of the GOTU assemblage associated with the seasons.     

Analysis of parasitic communities in fishes from Lake Baikal

Analysis of infracommunities and component communities of fish parasites in Lake Baikal has been conducted for the first time. It has been revealed that parasite infracommunities for the majority of Baikal fishes are weakly balanced and impoverished (the Berger-Parker Index is > 0.5; Evension is < 0.5; the Brillouin Index is < 1). The highest diversity and balance of the communities are characteristic for carnivorous fishes (Brachymystax lenok, Hucho taimen, Thymallus arcticus, Esox lucius, and Percafluviatilis). The component parasitic communities of Leuciscus leuciscus baicalensis, Rutilus rutilus, and Leocottus kesslerii are the most diverse in Lake Baikal since the Shennon index for L. leuciscus baicalensis, R. rutilus, and L. kesslerii is 2.4, for Paracotlus knerii--2.2, Limnocoitus godlewskii--2.3, Phoxinus phoxinus--2.1, Lota lota and Limnocuttus pallidus--1.9, P. fluviatilis--1.8, Leuciscus idus--1.8. The component parasitic communities of other fishes in Lake Baikal have low indices of biological diversity (H = 0.5-1.05, Smp is close to 1). A classification of mature and immature components of parasitic communities based on the ratio of specialist species and generalist species has been proposed. It is established that the component parasitic communities in sublitoral, profundal, and pseudoabyssal zones are mature, while in the littoral zone they are immature (impoverished and weakly balanced). The component parasitic communities in benthophagous fishes and predators are mature, in planktivorous fishes they are immature. The component parasitic communities are mature in the family Cyprinidae and immature in the families Coregonidae and Cottidae. The component parasitic communities of the Boreal Plain and Boreal Submountain faunal complexes are mature, but they are immature in Lake Baikal and Arctic freshwater complexes.     

Linking seasonal inorganic nitrogen shift to the dynamics of microbial communities in the Chesapeake Bay

Seasonal shifts of dissolved inorganic nitrogen (DIN) and the dynamics of microbial communities for nitrogen transformation were investigated in the water column of Chesapeake Bay. The relative abundance of nitrogen over phosphorus (N*) showed a strong seasonal and spatial pattern: gradually decreased from upstream to downstream; high in winter and low in summer. Because the phosphorus concentration remained relatively stable, the spatiotemporal pattern of N* implied that a substantial fraction of DIN was removed in the bay, especially in summer. Correlation analyses indicated the functional microbial communities and environmental variables, such as temperature, dissolved oxygen, salinity, played important roles for connecting the seasonal variation of N*. Among them, temperature was the trigger factor. High temperature in the summer induced the growth of functional microbes, which subsequently consumed a large portion of DIN inputted from the tributaries and reduced the N*. The current study provided the relative importance of microbial communities and environmental variables in driving the DIN loss in the bay.     

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

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

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.     

Parasitic chytrids: their effects on phytoplankton communities and food-web dynamics

Many phytoplankton species are susceptible to fungal parasitism. Parasitic fungi of phytoplankton mainly belong to the Chytridiomycetes (chytrids). Here, we discuss the progression made in the study of chytrids that parasitize phytoplankton species. Specific fluorescent stains aid in the identification of chytrids in the field. The established culturing methods and the advances in molecular science offer good potential to gain a better insight into the mechanisms of epidemic development of chytrids and coevolution between chytrids and their algal hosts. Chytrids are often considered to be highly host-specific parasites, but the extent of host specificity has not been fully investigated. Chytrids may prefer larger host cells, since they would gain more resources, but whether hosts are really selected on the basis of size is not clear. The dynamics of chytrids epidemics in a number of studies were partly explained by environmental factors such as light, temperature, nutrients, pH, turbulence and zooplankton grazing. No generalization was made about the epidemic conditions; some state unfavorable conditions for the host growth support epidemic development, while others report epidemics even under optimal growth conditions for the host. Phytoplankton is not defenseless, and several mechanisms have been suggested, such as a hypersensitivity response, chemical defense, maintaining a high genetic diversity and multitrophic indirect defenses. Chytrids may also play an important role in food webs, because zoospores of chytrids have been found to be a good food source for zooplankton.     

A survey of plant communities of springs and mountain brooks in Czechoslovakia

Up till now 22 plant associations of springs and mountain brooks are known in Czechoslovakia. They can be arranged in 6 alliances:Cardaminion amarae, Cardamino-Montion, Swertio-Anisothecion squarrosi, Cratoneuro filicini-Calthion laetae, Cratoneurion commutati andLycopo-Cratoneurion. Three alliances, two associations and one subassocíation are described as new ones, three associations are renamed.     

Macrozoobenthos assemblages in springs of the Penza region

Classification of spring macrozoobenthos assemblages was carried out using original data. Five types of assemblages were identified: Potamophylax nigricornis-Baetis rhodani-Cnetha spp.-Nemouridae, Rhyacophila fasciata; Stenophylax lateralis-Euglesidae-Ptychoptera spp.; Asellus aquaticus; Apatania auricular. The differentiation factors of these assemblages are water flow, water velocity, which are independent conditions, and substrate type. Comparison of classification with other variants of classification of spring macrozoobenthos found in the literature was carried out.     

Phytomonitoring of air pollution in the Baikal region

Phytomonitoring of air pollution has been performed using the Scots pine as a highly sensitive bioindicator. Needles have been sampled from key plots along the macrotransect Sayansk-Irkutsk-Listvyanka (with a total length of 320 km) covering the main industrial centers of the Baikal region and stretching up to the shoreline of Lake Baikal. The content of inorganic pollutants (sulfur, fluorides, heavy metals, etc.) has been determined. The highest level of air pollution has been registered in the following industrial centers: Angarsk, Irkutsk, Usol’e-Sibirskoe, and Shelekhov. The degree of pollution is lower in industrial centers such as Sayansk and Cheremkhovo. The data provide evidence that most pollutants reach the shoreline of Lake Baikal.     

Similarities and seasonal variations in bacterial communities from the blood of rodents and from their flea vectors

Vector-borne microbes are subject to the ecological constraints of two distinct microenvironments: that in the arthropod vector and that in the blood of its vertebrate host. Because the structure of bacterial communities in these two microenvironments may substantially affect the abundance of vector-borne microbes, it is important to understand the relationship between bacterial communities in both microenvironments and the determinants that shape them. We used pyrosequencing analyses to compare the structure of bacterial communities in Synosternus cleopatrae fleas and in the blood of their Gerbillus andersoni hosts. We also monitored the interindividual and seasonal variability in these bacterial communities by sampling the same individual wild rodents during the spring and again during the summer. We show that the bacterial communities in each sample type (blood, female flea or male flea) had a similar phylotype composition among host individuals, but exhibited seasonal variability that was not directly associated with host characteristics. The structure of bacterial communities in male fleas and in the blood of their rodent hosts was remarkably similar and was dominated by flea-borne Bartonella and Mycoplasma phylotypes. A lower abundance of flea-borne bacteria and the presence of Wolbachia phylotypes distinguished bacterial communities in female fleas from those in male fleas and in rodent blood. These results suggest that the overall abundance of a certain vector-borne microbe is more likely to be determined by the abundance of endosymbiotic bacteria in the vector, abundance of other vector-borne microbes co-occurring in the vector and in the host blood and by seasonal changes, than by host characteristics.     

Plant diversity and dry-matter dynamics of peri-urban plant communities in an Indian dry tropical region

The emergence of variety of land-use changes due to continuous anthropogenic pressure in peri-urban areas may concomitantly result in modification of the structure of associated plant communities for their sustainable growth. In the present study, plant diversity, and above- and belowground biomass distribution among species were investigated to understand their dynamics across different season, soil, and site conditions in a dry tropical peri-urban region in India. From four study sites that covered contrasting land uses: abandoned brick kiln (ABK), grazing land (GL), Kali river bank (KRB), and agricultural land (AL), a total of 360 monoliths were randomly extracted in three seasons, and dry weights were estimated for aboveground and belowground parts of species individuals. Seasonal soil samples of the sites were analyzed for physico-chemical characteristics. Of the total 87 recorded species that were mainly annual weeds and ruderals, 77% were forbs and 23% grasses. The ranges of plant biomass recorded across all sites and seasons were: aboveground 228–738 g m⁻², belowground 83–288 g m⁻², and a total of 344–1,026 g m⁻². The dominance of species differed between above- and belowground; some species dominated only above- or belowground, and others dominated in both layers. Above- and belowground biomass of the sites, differential community-biomass allocation to above- and belowground parts and species dominants varied significantly with site and season. ABK and AL sites showed lower species diversity and soil nutrients compared to GL and KRB sites. Belowground biomass significantly declined with increasing soil organic C and total N, indicating altered dry matter allocation under resource-scarce habitat conditions. Higher diversity occurred at both low- and high-biomass sites, reflective of enhanced ability of these plant communities to exploit resources maximally in spatio-temporal pattern.     

Ecotonal shifts in diversity and functional traits in zoobenthic communities of karst springs

We examined the potential importance of distance from the spring source (reach), season, and physicochemical variability on zoobenthic biodiversity, biomass, and trait-based metrics [functional feeding groups (FFG) and habit traits] in three karst spring systems in the Ozarks region of Missouri, USA. Density and biomass were measured during summer and winter in each spring source and three downstream reaches of each springbrook. Nearly 20,000 invertebrates in total were collected, identified, and counted. We measured biomass directly or by length–weight relationships. Overall downstream and seasonal patterns of diversity, biomass, and traits were similar among springs, but species dominance and composition varied significantly. Taxonomic richness increased downstream in all springs, but evenness decreased. Amphipods and isopods were the most abundant taxa at the spring source but were progressively replaced downstream by insects (with dominance varying among springs and seasons). Density and biomass for flatworms, snails, and insects increased downstream, while crustacean numbers diminished along this ecotone. FFG increased from 3 at the spring source (mostly shredders) to 4–7 downstream where scrapers, collectors, and/or predators predominated. Physicochemical factors proved minor at best as mechanistic explanations for ecotonal changes. We conclude that structural and functional community changes could be attributed to a matrix of interrelated factors including organic substrate, food availability, and biotic interactions.