Biogeography of testate amoebae in the soils of Mexico

We studied testate amoebae (testates) in the soils of coniferous and deciduous forests and in the wetland and aquatic habitats of Mexico. In 141 samples we found 205 taxa identified to the species or intraspecies level and 68 testate amoebae, which could not be identified to the species level. The highest species diversity of testates was found in the soils of the tropical rainforest (126 species and intraspecific taxa, including spp.) and in tropical wetlands (144 species and intraspecific taxa, including spp.). The study documented testate amoebae with a limited geographical distribution (genera Centropyxis, Cornuapyxis, Ellipsopyxis, Hoogenraadia, Planhoogenraadia, Apolimia, Certesella, Apodera, and Alocodera). We found that testate amoebae in the soils of Mexico had a high level of polymorphism and individual variability. We discuss the value of soil testate amoebae for defining biogeographical regions of Mexico.     

Plants and testate amoebae as environmental indicators in cupriferous peatlands,New Brunswick,Canada

Vegetation, testate amoebae, and metal concentrations in water and soil (mostly peat) were studied in two copper-rich treed swamps located north of Sackville, New Brunswick, Canada. One of the sites is partly disturbed, characterized by bare soil nearly devoid of vegetation cover except for isolated patches of the moss species, Pohlia nutans, around seepages and small streams. Copper concentrations in soil and water samples were high but varied among plots. Values in soil samples were as high as 16,000 μg/g in the open area, with 4550 μg/g being the mean. The highest value in groundwater was 1540 μg/l, with 292 μg/l being the mean. Twenty-seven testate amoebae species were identified from soil samples. The most abundant species were Cyclopyxis arcelloides and Centropyxis spp. Principal component analysis and detrended correspondence analysis showed that their abundance was especially high in the open area where copper concentrations were high, while species diversity of testate amoebae was low in the open area. This study suggests potential use of mosses and testate amoebae as bio-indicators and bio-monitoring tools for metals such as copper.     

Diversity and Distribution of Freshwater Testate Amoebae (Protozoa) Along Latitudinal and Trophic Gradients in China

Freshwater microbial diversity is subject to multiple stressors in the Anthropocene epoch. However, the effects of climate changes and human activities on freshwater protozoa remain poorly understood. In this study, the diversity and distribution of testate amoebae from the surface sediments were investigated in 51 Chinese lakes and reservoirs along two gradients, latitude and trophic status. A total of 169 taxa belonging to 24 genera were identified, and the most diverse and dominant genera were Difflugia (78 taxa), Centropyxis (26 taxa) and Arcella (12 taxa). Our analysis revealed that biomass of testate amoebae decreased significantly along the latitudinal gradient, while Shannon-Wiener indices and species richness presented an opposite trend (P?P?相似文献   

Archaeal and bacterial diversity in two hot spring microbial mats from a geothermal region in Romania

The diversity of archaea and bacteria was investigated in two slightly alkaline, mesophilic hot springs from the Western Plain of Romania. Phylogenetic analysis showed a low diversity of Archaea, only three Euryarchaeota taxa being detected: Methanomethylovorans thermophila, Methanomassiliicoccus luminyensis and Methanococcus aeolicus. Twelve major bacterial groups were identified, both springs being dominated by Cyanobacteria, Chloroflexi and Proteobacteria. While at the phylum/class-level the microbial mats share a similar biodiversity; at the species level the geothermal springs investigated seem to be colonized by specific consortia. The dominant taxa were filamentous heterocyst-containing Fischerella, at 45 °C and non-heterocyst Leptolyngbya and Geitlerinema, at 55 °C. Other bacterial taxa (Thauera sp., Methyloversatilis universalis, Pannonibacter phragmitetus, Polymorphum gilvum, Metallibacterium sp. and Spartobacteria) were observed for the first time in association with a geothermal habitat. Based on their bacterial diversity the two mats were clustered together with other similar habitats from Europe and part of Asia, most likely the water temperature playing a major role in the formation of specific microbial communities that colonize the investigated thermal springs.     

Macroinvertebrate communities of karst springs of two river catchments in the Southern Limestone Alps (the Julian Alps, NW Slovenia)

The macroinvertebrate communities of 16 karst springs in the Southern Limestone Alps (Slovenia, SE Europe), were studied from May to September 1999, together with the major chemical parameters of the water and selected physical characteristics of the springs. The springs are located in an area of 800 km², between 410 and 955 m a.s.l., and drain into two rivers whose catchments are separated by mountain ranges up to 2864 m. The Soča river drains into the Adriatic Sea and the Sava into the Black Sea. Springs showed relatively large fluctuations in discharge and small variations in temperature (normally about 1 °C) during the period of study. Seventy macroinvertebrate taxa were collected. Chironomidae (Diptera), Limnephilidae (Trichoptera), Enchytraeidae (Oligochaeta), Tricladida (Turbellaria) and Belgrandiella kuesteri (Gastropoda) were the most widespread taxa, collected from the majority of sampling sites. The environmental characteristics showed a great heterogeneity, and there was a large variation in the taxonomic composition and relative abundance of taxa between springs and during seasons. The coexistence of taxa with highly divergent ecological requirements is characteristic of the spring communities studied. They range from stygobionts and spring-restricted species to ubiquitous species. The differences observed in spring fauna in the two river catchments were probably dictated by differences in local environmental parameters and not by the geographical location in the different river catchments.     

Ectomycorrhizal fungal community of naturally regenerated European larch (Larix decidua) seedlings

An investigation was undertaken to assess the community structure of ectomycorrhizal (ECM) fungi on naturally regenerating European larch (Larix decidua Mill.) seedlings grown under forest conditions. The sites examined were in two managed monoculture larch forests, differentiated by soil chemistry and mature tree density. Morphological and molecular analyses revealed a total of 22 fungal taxa. From detected ECM fungal taxa, 13 were noted at Site I and 13 at Site II. Only four taxa were found in both sites (Russula ochroleuca, Thelephora terrestris, Lactarius tabidus and Paxillus involutus). The most abundant species at Site I (lower mineral concentration, high tree density) was Hydnotrya tulasnei (25.7?%), followed by Pseudotomentella tristis, Tomentella sublilacina and Russula puelaris. At Site II (higher mineral concentration, low tree density) the dominant fungal symbiont of larch seedlings was clearly Wilcoxina mikolae, which accounted for 74?% of mycorrhizal tips. The less abundant species comprised T. terrestris, L. tabidus, Xerocomus pruinatus and R. ochroleuca. The analysis of similarity (ANOSIM) and non-metric multidimensional scaling (NMDS) ordination clearly separated the ECM fungal assemblages in the two sites tested. Because our study sites were differentiated by many factors, it is not easy to distinguish one factor in particular to explain the differences observed between the ECM communities at Sites I and II. The results obtained significantly increase our knowledge about the diversity of the ECM fungi hosted by L. decidua. The large number of ECM fungi detected was the first observation showing these fungi as symbiotic partners of European larch.     

From spring sources to springbrook: Changes in environmental characteristics and benthic fauna

Spatial patterns in macroinvertebrate communities and some abiotic factors were examined in three rheocrene springs and their springbrooks (Kraków-Cz?stochowa Upland, southern Poland). The mean discharge of particular springs ranged from 5 to 11 L s^?1, and its annual fluctuations were small. Water temperature was very stable at all sampling sites. In the eucrenon the number of benthic taxa was the smallest (9–14 determined to the family level), but the densities were the highest (approx. 14000 ind. m^?2). The biggest changes in macroinvertebrate composition were observed in the modified hypocrenon, which is an artificial pond. The lowest number of taxa were found in a natural, short springbrook with a nondiversified bottom substrate. The density of crenophilic taxa (Drusus trifidus, Dugesia gonocephala, Elmidae) diminished along the springbrooks, while the opposite trend was observed for ubiquitous taxa (some Oligochaeta, Asellus aquaticus and Chironomidae). Even in a very short natural springbrook (30 m), Drusus trifidus, the only species of Trichoptera found in the springs discussed here, goes through the entire development cycle. The strongest influence of a big river was observed at the outflow of one of the natural springbrooks, where the highest number of riverine oligochaete species were found. The benthic fauna of the springs studied here differed from that found in other springs in this area — the absence of the typical crenophilic species Bithynella austriaca (Gastropoda) and the presence of Gianus aquedulcis (Oligochaeta) may indicate the autonomy of the spring fauna in the Mstów area, possibly resulting from the postglacial geomorphological formation of this region or differences in habitat conditions.     

Granulometric and geomorphological characteristics of Rezu Khal canal,Bangladesh: Inferences for sustainable ecosystem and management

The geomorphology and sedimentological characteristics can build the sustainable ecosystem according to the existing environment. The present study concentrates on the findings of the total network of RezuKhal at the Cox's Bazar district that includes data on geomorphologic features and sediment characteristics. We used Geographical Information System (GIS) as a suitable method which depicts the process of data collection, data management, preparation, and map representation using ArcGIS software. The total catchment area of RezuKhal is estimated as 140 sq.km in Bangladesh. The data includes geomorphologic parameters and sediment obtained from samples collected in three sites (A, B, and C) in the catchment area of Rezu Khal. The sampling was performed in each station in every month of the hydrological year 2013. The key map indicates that one of the major rivers drains from Myanmar, 3 tributaries from Ukhia Upazilla and the other two originate from Ramu Upazila. These rivers were identified crisscrossed on the long plain land. The total length of the main river was 43.46 sq.km and the length of major tributaries 65.41 sq.km, while the total length of major sub-tributaries are 40.69 sq. km. The analysis of the sedimentation of the Rezu Khal area demonstrated that it is dominated by fine sand and very fine sand in the main river and the different tributaries. Morphologically, the study domain can set on the three sites, including, Site A (estuarine part), Site B (long plain land area) and Site C (bottom of the hilly area). The sedimentological part in this study included concentration of sediment temperature (S-temp, 24–33°C), SOC 0.29% and 4.485%, (SOM) fluctuated between 0.51% and 7.73%. The average sediment texture properties values are 49.57 ± 0.01, 25.38 ± 0.01, 11.55 ± 0.02 Furthermore, it has been grouped as medium sand, medium silt, and field water capacity, which varied significantly in different seasons and sites (p < 0.05). The substantial variation was found in temperature, coarse silt, and sediment pH in terms of sites (p < 0.01), while PO4-P change with seasons (p < 0.05). Organic matter, organic carbon, and nutrients were gathered in the mouth of the estuary and formed a unique sand dune habitat which provided food and nutrients for benthic aquatic fauna. The sediment characteristics were significantly affected by its seasonal variation and human activities of Rezu Khal. The tributaries and its sub-tributaries of Rezu Khal have different applications with their unique environment, such as agriculture, irrigation, pisciculture, drinking and sand collection, etc. The qualitative and quantitative findings of the present study can estimate the existing resources of the Rezu Khal.     

Toxigenic algae and associated phycotoxins in two coastal embayments in the Ebro Delta (NW Mediterranean)

Harmful Algal Bloom (HAB) surveillance is complicated by high diversity of species and associated phycotoxins. Such species-level information on taxonomic affiliations and on cell abundance and toxin content is, however, crucial for effective monitoring, especially of aquaculture and fisheries areas. The aim addressed in this study was to determine putative HAB taxa and related phycotoxins in plankton from aquaculture sites in the Ebro Delta, NW Mediterranean. The comparative geographical distribution of potentially harmful plankton taxa was established by weekly field sampling throughout the water column during late spring–early summer over two years at key stations in Alfacs and Fangar embayments within the Ebro Delta. Core results included not only confirmed identification of HAB taxa that are common for the time period and geographical area, but also provided evidence of potentially new taxa. At least 25 HAB taxa were identified to species level, and an additional six genera were confirmed, by morphological criteria under light microscopy and/or by molecular genetics approaches involving qPCR and next generation DNA pyrosequencing. In particular, new insights were gained by the inclusion of molecular techniques, which focused attention on the HAB genera Alexandrium, Karlodinium, and Pseudo-nitzschia. Noteworthy is the discovery of Azadinium sp., a potentially new HAB species for this area, and Gymnodinium catenatum or Gymnodinium impudicum by means of light microscopy. In addition, significant amounts of the neurotoxin domoic acid (DA) were found for the first time in phytoplankton samples in the Ebro Delta. While the presence of the known DA-producing diatom genus Pseudo-nitzschia was confirmed in corresponding samples, the maximal toxin concentration did not coincide with highest cell abundances of the genus and the responsible species could not be identified. Combined findings of microscopic and molecular detection approaches underline the need for a synoptic strategy for HAB monitoring, which integrates the respective advantages and compensates for limitations of individual methods.     

Ecological description of the sodium chloride mineral springs in the Kirenga River basin and the upper reaches of the Lena River: 2. Flora of non-vascular plants: Algae,lichens

For the first time, the flora of algae and aquatic lichens is studied in the sodium chloride mineral springs of the Northern Baikal region flowing from the Lower Cambrian salt-bearing formations. The full list of algae found in six springs is presented. In total, 257 taxa are identified belonging to six divisions: Cyanoprokaryota (=Cyanophyta), Euglenophyta, Bacillariophyta, Xanthophyta, Chlorophyta, and Streptophyta. The flora of diatoms is the richest (196 taxa, or 76%). The similarity of algoflora of different springs is negligible. Species that are indifferent to salinity prevail in most of the mineral springs; mesohaline species dominate in the Ust’-Kutskii spring. Nineteen taxa of halophile diatoms are identified. The marine species Percursaria percursa (Chlorophyta) is recorded in Klyuchevskoi and Ust’-Kutskii springs. In the three springs, seven lichen species from the four genera are identified, five species are truly aquatic and two species may stand flooding; all these species are found in the freshwater ponds and streams. Two species of the genus Bagliettoa are probably relict in the Baikal region.     

Genome-wide identification, classification and expression analysis of genes encoding putative fasciclin-like arabinogalactan proteins in Chinese cabbage (Brassica rapa L.)

Fasciclin-like arabinogalactan proteins (FLAs), a subclass of arabinogalactan proteins (AGPs), have both predicted AGP-like glycosylated regions and putative fasciclin (FAS) domains, which may function in cell adhesion and communication. Previous studies have identified 21, 27, and 34 FLAs in Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and wheat (Triticum aestivum), respectively. In this study, we identified 33 FLAs in the annotated genome of Chinese cabbage (Brassica rapa ssp. pekinensis line Chiifu-401-42). Sequence analysis indicated that FAS domains each contain two highly conserved regions, named H1 and H2, and that 17 FLAs from B. rapa (BrFLAs) possess both of these regions. Prediction of glycosylphosphatidylinositol (GPI) modification sites suggested that 15 BrFLAs were GPI-anchored to the plasma membrane. Additionally, 25 BrFLAs may have been duplicated during the processes that shaped the triplicated genome of the mesopolyploid B. rapa. Expression analyses indicated that BrFLA1, BrFLA11, BrFLA13, BrFLA28 and BrFLA32 were specifically expressed in inflorescence. Meanwhile, BrFLA9 (homologous to AtFLA12) is specifically expressed in stem, and BrFLA6/22 (homologous to AtFLA11) is also highly expressed in stem, suggesting BrFLA6/9/22 may have the same functions as AtFLA11/12 in A. thaliana. Taken together, the identification and bioinformatic analysis of FLAs in B. rapa will open the way for studying their biological functions in plant growth and development as well as evolutionary history of this gene family from A. thaliana to B. rapa.     

PCR Detection and Analysis of the Free-Living Amoeba Naegleria in Hot Springs in Yellowstone and Grand Teton National Parks

Free-living thermotolerant amoebae pose a significant health risk to people who soak and swim in habitats suitable for their growth, such as hot springs. In this survey of 23 different hot springs in Yellowstone and Grand Teton National Parks, we used PCR with primer sets specific for Naegleria to detect three sequence types that represent species not previously described, as well as a fourth sequence type identified as the pathogen Naegleria fowleri.     

Comparative ecology of vascular plant,bryophyte and testate amoeba communities in four Sphagnum peatlands along an altitudinal gradient in Switzerland

Monitoring tools are needed to assess changes in peatland biotic communities and ecosystem functions in response to on-going climate and other environmental changes. Although the responses of soil organisms and plants to ecological gradients and perturbations do not always correlate, peatland monitoring is mainly based on vegetation surveys. Testate amoebae, a group of protists, are important contributors to carbon and nitrogen cycling in organic soils and are useful bioindicators in peatland ecology and paleoecology. There is however little comparative data on the value of testate amoebae, vascular plants and bryophytes as bioindicators of micro-environmental gradients in peatlands.We compared the relationships of testate amoebae, bryophytes, and vascular plants with soil temperature, water table depth, micro-habitats and the carbon and nitrogen content of Sphagnum mosses in four peatlands along a 1300 m altitudinal gradient in Switzerland. We used the full diversity of vascular plants and bryophyte but only a selection of ten easily identifiable testate amoeba morpho-taxa (i.e. species or species-complexes).Indirect and direct gradient ordinations, multiple factor analysis (MFA) and transfer function models for inferring water table depth showed that a selection of ten testate amoeba taxa are more powerful (% variance explained in RDA) and accurate (discrimination among habitats) indicators of local conditions (micro-habitat type, water table depth and Sphagnum C/N ratio) than the vegetation (vascular plants and bryophytes either individually or combined and considering the full diversity).Our study showed that a limited list of ten easily identifiable testate amoeba taxa have higher bioindication value than the full bryophytes and vascular plants. Furthermore, testate amoebae can be analyzed on samples collected at any season (accessibility allowing and if precise sampling sites are well marked) – a clear advantage for biomonitoring and can be used to infer past changes from the peat record at the same taxonomic resolution. This simple approach could therefore be very useful for biomonitoring of peatlands.     

The influence of habitat structure and flow permanence on invertebrate communities in karst spring systems

The macroinvertebrate fauna of five karst (limestone) springbrook systems with contrasting physical habitat and discharge patterns were investigated to examine the role of flow permanence and habitat structure on macroinvertebrate community composition. Clear physical differences were identified between perennial and intermittent springs and individual sampling stations. However, flow permanence, water temperature and the input of leaf litter exerted a greater influence on the aquatic invertebrate community than habitat structure. Perennial sites were characterised by a greater abundance of macroinvertebrates and greater Ephemeroptera, Plecoptera and Trichoptera (EPT) richness than intermittent sites. The fauna of all of the springbrook systems examined were dominated by relatively common and ubiquitous taxa (e.g. Gammarus pulex) although a number of taxa displaying life cycle adaptations to ephemeral aquatic habitats (e.g. Limnephilus auricula and Stenophylax permistus) were recorded at intermittent sites.     

Distribution of live benthic Foraminifera at three oceanographically dissimilar sites in the northeast Atlantic: preliminary results

Live (i.e. rose Bengal stained) benthic foraminiferal assemblages in the 0–1 cm layer of multiple core samples were examined at three contrasting sites in the northeast Atlantic as part of the Natural Environment Research Council Deep Ocean Benthic Boundary Layer (BENBO) Thematic Programme. Sites A (3600 m water depth) and C (1900 m) were located in the Rockall Trough while Site B (1100 m) was in the Hatton–Rockall Basin. Wet-sorting sediment residues (>125 m fraction) revealed more abundant (98–190 individuals/10 cm²) and diverse (71–99 species /27 cm²) assemblages than found previously in studies employing dry-sorting techniques. At all three sites, the assemblages were numerically dominated by delicate soft-bodied and agglutinated species, most of which are undescribed. Calcareous taxa formed a relatively small proportion of the assemblages (23% of individuals at Site B, 13% at Site C and 7% at Site A). Conversely, the agglutinated hormosinaceans (mainly Reophax species) became more prominent with increasing depth and accounted for 8% of the assemblage at Site B, 33% at Site C and 51% at Site A. Foraminifera represented 67–81% of the fauna in the samples and greatly outnumbered the metazoans. The assemblage at Site A has similarities with abyssal assemblages, while those at Sites B and C contain characteristic bathyal species. At Site B, Uvigerina peregrina and Melonis barleeanum are abundant, suggesting that there are high organic carbon inputs at this site. Reduced species diversity was observed at Site A following the spring phytodetritus bloom due to the presence of large numbers of juvenile Hoeglundina elegans, although it is not clear whether this species is responding to phytodetritus inputs.     

Middle Eocene–late Oligocene climate variability: Calcareous nannofossil response at Kerguelen Plateau,Site 748

A major deterioration in global climate occurred through the Eocene–Oligocene time interval, characterized by long-term cooling in both terrestrial and marine environments. During this long-term cooling trend, however, recent studies have documented several short-lived warming and cooling phases. In order to further investigate high-latitude climate during these events, we developed a high-resolution calcareous nannofossil record from ODP Site 748 Hole B for the interval spanning the late middle Eocene to the late Oligocene (~ 42 to 26 Ma). The primary goals of this study were to construct a detailed biostratigraphic record and to use nannofossil assemblage variations to interpret short-term changes in surface-water temperature and nutrient conditions. The principal nannofossil assemblage variations are identified using a temperate-warm-water taxa index (Twwt), from which three warming and five cooling events are identified within the middle Eocene to the earliest Oligocene interval. Among these climatic trends, the cooling event at ~ 39 Ma (Cooling Event B) is recorded here for the first time. Variations in fine-fraction δ¹⁸O values at Site 748 are associated with changes in the Twwt index, supporting the idea that significant short-term variability in surface-water conditions occurred in the Kerguelen Plateau area during the middle and late Eocene. Furthermore, ODP Site 748 calcareous nannofossil paleoecology confirms the utility of these microfossils for biostratigraphic, paleoclimatic, and paleoceanographic reconstructions at Southern Ocean sites during the Paleogene.     

Phenotypic characterization and molecular taxonomic studies on Bacillus and related isolates from Phragmites australis periphyton

Reeds may play important role in the self-purification of aquatic habitats due to the filtration capacity and their periphyton communities developing on the underwater plant surfaces. The efficiency of this process and the transformation of organic substances can be influenced by the species composition and activity of microbial communities, including Bacillus and related species. For cultivation based bacteriological examinations reed periphyton samples were collected from 30 cm beneath the water surface of Lake Velencei and the Soroksár Danube branch (Hungary). After a primary selection 40 Bacillus and related strains were investigated by traditional morphological, biochemical tests, API 20E, API 50CHB and BIOLOG GP2 systems, and identified by 16S rDNA sequence comparison. The isolated strains were characterized by wide biochemical activity spectrum (i.e., the metabolism of carbohydrates and biopolymers) as well as widespread ecological tolerance based on their NaCl and pH range investigations. Species with facultative alkaliphilic features (Marinibacillus marinus, Bacillus firmus) were detected only from the reed biofilm of Lake Velencei, while alkalitolerant Bacillus and related species from both sampling sites. 22 endospore-forming strains were identified as members of species B. cereus, B. firmus, B. flexus, B. licheniformis, B. megaterium, B. muralis, B. pumilus, B. subtilis and Marinibacillus marinus. Only one species, with 95–96% sequence similarities to B. pumilus was found to be common among the strains from Lake Velencei and the Soroksár Danube branch. Altogether, 18 strains could not be identified as known species of Bacillus, Brevibacillus and Paenibacillus, hence they may represent new bacterial taxa.     

The temporal and spatial distribution, composition and abundance of Protozoa in Chaohu Lake, China: Relationship with eutrophication

Systematic investigations into the temporal and spatial distribution, composition and abundance of protozoa in two regions with different trophic levels in Chaohu Lake, a large, shallow and highly eutrophic freshwater lake in China, were conducted during 2002–2003. A total of 114 species of protozoa, including phytomastigophorans, zoomastigophorans, amoebae and ciliates, were identified from 120 polyurethane foam unit (PFU) samples exposed at four stations and from various types of natural substrates. Of the 114 taxa, 36 core species were found on PFU substrates and 23 of these were found on natural ones. Protozoan abundance and chemical–physical parameters at nine sampling stations, four in the western lake and five in the eastern part, indicate trophic gradient changes along the lake. Seasonal variations in the species composition of major groups at littoral PFU sampling stations illustrate the effect of a severe algal bloom on the protozoan community structure. Temporal and spatial distributions of individual abundance as functions of water temperature and trophic status were revealed. This study demonstrates again that the PFU artificial substrate method samples protozoan communities more effectively than routine natural substrate methods.