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.     

Organotrophic bacteria of the Baikal Rift Zone hot springs

Pyrosequencing of the 16S rRNA gene fragments was used to investigate the bacterial community of an Alla hot spring microbial mat. The mat community was mainly represented by the members of five phyla: Deinococcus-Thermus, Nitrospirae, Atribacteria (OP9), Proteobacteria, Chloroflexi, and Firmicutes, with other groups responsible for not more than 2% of the total number. From hot springs of the Baikal Rift Zone (Buryatia, Russia), 13 strains of aerobic alkaliphilic thermophilic organotrophic bacteria were isolated, and their morphology, ecology, physiology, and phylogenetic position were studied. Based on analysis of their 16S rRNA gene sequences, the isolates were identified as members of the family Bacillaceae. Strains Al-9-1, Se-1, Ga-1-1, Ga-9-2, and Se-1-10 were assigned to the genus Anoxybacillus; strains Ur-6, Br-2-2, А2, and Um-09m, to the genus Bacillus; strains Gor-10s and Gа-35, to the genus Paenabacillus. Secreted endopeptidases of the isolates were shown to have relatively narrow substrate specificity. The investigated enzymes were characterized by high pH (6.3–11.4) and temperature stability (23–70°C), which makes it possible to carry out organic matter degradation in the environment under variable ecological conditions.     

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.     

克氏针茅(Stipa krylovii)草原土壤呼吸及其影响因子

基于LI6400-09便携式光合作用测量系统的土壤呼吸观测系统对内蒙古克氏针茅(Stipa krylovii)草原2005年5月至9月的土壤呼吸作用的测定结果,研究了克氏针茅草原土壤呼吸速率的日、生长季动态及其控制因子.结果表明,在生长季节,克氏针茅草原土壤呼吸速率的日季动态均呈单峰型变化;日最大值和最小值分别出现在10:00～13:00和凌晨4:00左右;生长季日均最大值(0.14mgCO2m-2s-1)出现在6月份,日均最小值(0.03mgCO2m-2s-1)出现在8月份.在日尺度上,随着生长期的变化,控制土壤呼吸作用的环境因子有所不同;在生长初期和末期土壤呼吸速率的限制因子主要为总辐射,而在生长中期,控制因子则为气温和土壤含水量.在整个生长季的尺度上,极显著影响土壤呼吸作用的环境因子则为土壤含水量(0～10cm、10～20cm、20～30cm)、总辐射和气温.约有72%的土壤呼吸作用生长季变异是由表层土壤含水量和总辐射共同决定的,其中0～10cm土壤含水量是影响克氏针茅草原土壤呼吸作用在生长季节变化的主导环境因子,可以单独解释土壤呼吸作用变异的51%.     

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.     

Characteristics of softwater streams in Rhode Island II. Composition and seasonal dynamics of macroalgal communities

Forty stream segments in Rhode Island, U.S.A., were examined seasonally from June 1979 to March 1982. Thirty-nine species of macroalgae were collected, respresenting 25 genera. The composition of the lotic flora was 54% green algae, 31% red algae, 5% blue-green algae, 5% xanthophytes, 3% chrysophytes and 3% diatoms. The majority of these taxa (85%) were filamentous. From a biweekly examination of five stream segments, macroalgal communities could be grouped according to light regime. Species in unshaded streams exhibited little seasonality, whereas in streams shaded by one or more layers of riparian canopy, maxima in species numbers and abundance occurred during colder seasons. The most widespread and abundant species were the blue-green alga Phormidium retzii, the green alga Draparnaldia acuta, and the diatom Eunotia pectinalis. P. retzii and E. pectinalis were aseasonal annuals, while D. acuta was primarily a winter-spring form. It appears that pH is a major factor affecting broad geographic distribution patterns of stream macroalgae, whereas the light regime established by overhanging canopy is an important factor which influences localized abundance and seasonality of lotic macroalgal communities. Niche pre-emption appears to be a common mode of resource space division among stream macroalgae in Rhode Island. E. pectinalis is the strongly developed dominant in this drainage system.     

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.     

水盾草入侵沉水植物群落的季节动态

水盾草(cabomba caroliniana)是原产美国和南美巴西等地的多年生植物。自1993年作为新记录报道以来,在中国华东水网地带大面积扩散,并在江苏太湖流域、浙江杭嘉湖平原、宁绍平原等水域成为很多沉水植物群落的优势种。课题组在其分布区的苏州太湖乡、湖州道场乡、杭州五常乡、绍兴陶堰镇、柯岩镇和宁波方桥镇等6个地点设置固定样地对水盾草入侵群落进行了9个季节的调查,分析了不同季节群落种类组成与生物量的变化等。结果表明：各群落优势种在不同季节有变化,有些群落在所调查季节中主要优势种都为水盾草(五常乡、柯岩镇和方桥镇),另一些群落优势种则发生季节及年际变化(太湖乡、道场乡和陶堰镇),如太湖乡冬季优势种均为菹草、其它季节为水盾草。水盾草的生物量在样地、季节间变化很大,最高一般在秋季,变幅达近50倍。水盾草生物量的季节动态显示3种情况：一是由于人为干扰大幅下降,二是处于相对稳定的平衡状态,三是大幅上升。其中后两种情况下人为干扰较小,是群落自身演替的结果。从种类组成来看,种类组成单一的群落,水盾草重要值均在50％以上;种类组成复杂的群落,其重要值随季节而变化。说明群落物种丰度与其对水盾草的易感性间有较密切的联系,水盾草易于入侵组成单一的群落,并迅速成为优势种。本地种与水盾草的生物量最大值出现在不同水深下,水盾草的最适生长水深在1．6m左右的水域,而本地种金鱼藻、苦草和黑藻的最适水深在0．8～1m左右。水盾草4个季节最适水深比本地种都要大,表明在它们在沉水植物群落中处于不同生态位。较低的群落物种多样性与空间生态位空缺可能是水盾草成功入侵的主要原因。清淤等人为控制是防治水盾草入侵成功的有效手段,但这也将使本地种的生存受到威胁。     

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.     

Zooplankton seasonal dynamics in 2005–2007 at the eastern coast of southern Baikal,near the Pulp-and-Paper plant

The study investigated zooplankton seasonal dynamics in the pelagic and shelf zones at the eastern coast of Lake Baikal, near the Baikal Pulp-and-Paper Plant, in August and September of 2005, 2006, and 2007. It was shown that zooplankton development in the 0–50 mdepth over the study period followed a characteristic Baikal pattern despite increased industrial pressure on the study site.     

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.     

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.     

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.