Changes in riverine benthic diatom community structure along a chloride gradient

The application of salt is the primary means of deicing roads and highways in colder regions of north-eastern North America. This has increased the chloride concentrations of many lake and stream ecosystems. While this salinization has been documented, less is known about how increased salinity alters benthic communities in downstream ecosystems. Natural thresholds, at which there are large scale changes in community composition, have not yet been established for many types of contaminants, including chloride. The diatom community, which is sensitive to small changes in the ambient environment, has the potential to be a strong indicator of salinization effects on stream ecosystems. In this study, we sampled diatom communities in 41 streams across a salinity gradient throughout south central Ontario, Canada. We sampled benthic diatom assemblages in early May following complete snowmelt, when stream water chloride concentrations ranged from 5 to 502 mg/L. Based on redundancy analysis, we confirmed a strong association between the species composition of the diatom community and water conductivity, a commonly used index of stream salinity. Taxa indicator threshold analyses (TITAN) indicated the community changed substantially at chloride concentrations greater than 35 mg/L. We also found that, an indicator taxa, Meridion circulare, was extremely sensitive to high concentrations of salt and negatively correlated with chloride. In a wide synoptic survey of streams of our region, we found that streams in most developed watersheds exceed tolerance thresholds for benthic diatom communities. This work suggests that current chloride concentrations in urban watersheds are greatly exceeding the benthic community thresholds, for which improved management and regulatory practices are needed. Salinization thus appears to be an important feature of urban streams and needs to be considered as an important ecological driver in future studies.     

Changes in the community structure of ammonia-oxidizing bacteria during secondary succession of calcareous grasslands

The community structure of β-subclass Proteobacteria ammonia-oxidizing bacteria was determined in semi-natural chalk grassland soils at different stages of secondary succession. Both culture-mediated (most probable number; MPN) and direct nucleic acid-based approaches targeting genes encoding 16S rRNA and the AmoA subunit of ammonia monooxygenase were used. Similar shifts were detected in the composition of the ammonia oxidizer communities by both culture-dependent and independent approaches. A predominance of Nitrosospira sequence cluster 3 in early successional fields was replaced by Nitrosospira sequence cluster 4 in late successional fields. The rate of this shift differed between the two areas examined. This shift occurred in a background of relative stability in the dominant bacterial populations in the soil, as determined by domain-level polymerase chain reaction–denaturing gradient gel electrophoresis (PCR–DGGE). Molecular analysis of enrichment cultures obtained using different ammonia concentrations revealed biases towards Nitrosospira sequence cluster 3 or Nitrosospira sequence cluster 4 under high- or low-ammonia conditions respectively. High-ammonia MPNs suggested a decease in ammonia oxidizer numbers with succession, but low-ammonia MPNs and competitive PCR targeting amoA failed to support such a trend. Ammonia turnover rate, not specific changes in plant diversity and species composition, is implicated as the major determinant of ammonia oxidizer community structure in successional chalk grassland soils.     

Seasonal and annual reoccurrence in betaproteobacterial ammonia-oxidizing bacterial population structure

Microbes exhibit remarkably high genetic diversity compared with plant and animal species. Many phylogenetically diverse but apparently functionally redundant microbial taxa are detectable within a cubic centimetre of mud or a millilitre of water, and the significance of this diversity, in terms of ecosystem function, has been difficult to understand. Thus it is not known whether temporal and spatial differences in microbial community composition are linked to particular environmental factors or might modulate ecosystem response to environmental change. Fifty-three water and sediment samples from upper and lower Chesapeake Bay were analysed in triplicate arrays to determine temporal and spatial patterns and relationships between ammonia-oxidizing bacterial (AOB) communities and environmental variables. Thirty-three water samples (three depths) collected during April, August and October, 2001-2004, from the oligohaline upper region of the Bay were analysed to investigate temporal patterns in archetype distribution. Using a combination of a non-weighted discrimination analysis and principal components analysis of community composition data obtained from functional gene microarrays, it was found that co-varying AOB assemblages reoccurred seasonally in concert with specific environmental conditions, potentially revealing patterns of niche differentiation. Among the most notable patterns were correlations of AOB archetypes with temperature, DON and ammonium concentrations. Different AOB archetypes were more prevalent at certain times of the year, e.g. some were more abundant every autumn and others every spring. This data set documents the successional return to an indigenous community following massive perturbation (hurricane induced flooding) as well as the seasonal reoccurrence of specific lineages, identified by key functional genes, associated with the biogeochemically important process nitrification.     

封闭循环养殖系统中β变形菌亚纲氨氧化细菌的引物特异性

摘要:【目的】为探讨4 对不同的引物对封闭循环养殖系统生物膜中β 变形菌亚纲氨氧化细菌(β-AOB) 的特异性差异。【方法】采用16S rDNA 文库克隆技术对β-AOB 的多样性进行了分析。【结果】以引物CTO189f/CTO654r 扩增构建的文库中所含β-AOB 比例最高,可达67. 3%。不同封闭循环养殖系统的生物膜对引物的扩增效率有明显的影响,其中以养殖尼罗罗非鱼的封闭循环养殖系统生物膜为DNA 来源的,引物均有较高的扩增效率。【结论】针对封闭循环养殖系统生物膜中的β-AOB,特异性最高的是CTO189f /CTO654r 引物。     

Functionally distinct communities of ammonia-oxidizing bacteria along an estuarine salinity gradient

The relationship between ammonia-oxidizing bacteria (AOB) and potential nitrification rates was examined along a salinity gradient in a New England estuary in spring and late summer over 3 years. Ammonia-oxidizing bacteria abundance was estimated by measuring gene copies of the ammonia monooxygenase catalytic subunit (amoA) using real-time polymerase chain reaction. Ammonia-oxidizing bacteria abundance ranged from below detection to 6.0 x 10(7)amoA copies (gdw sediment)(-1). Mean potential nitrification rates ranged from 0.5 to 186.5 nmol N (gdw sediment)(-1) day(-1). Both AOB abundance and potential rates were significantly higher in spring than late summer. Correlations between rates and abundance varied significantly among sites, but showed site-specific ammonia oxidation kinetics related to AOB community structure. The effect of salinity on potential nitrification rates was evaluated by incubating sediment from each site under four salinity conditions (0, 5, 10 and 30 psu). At all sites, rates were generally highest in the intermediate salinity treatments, but rates at the upstream site were inhibited at high salinity, while rates at the two downstream sites were inhibited at the lowest salinity. Although salinity appears to be an important factor in determining AOB distribution, it may not be the primary factor as AOB exhibited a broad range of salinity tolerance in our experiments. Our results indicate that there are significant differences in abundance and community composition of AOB along the salinity gradient, and the differences are reflected in community function.     

Influences of infaunal burrows on the community structure and activity of ammonia-oxidizing bacteria in intertidal sediments

Influences of infaunal burrows constructed by the polychaete (Tylorrhynchus heterochaetus) on O(2) concentrations and community structures and abundances of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in intertidal sediments were analyzed by the combined use of a 16S rRNA gene-based molecular approach and microelectrodes. The microelectrode measurements performed in an experimental system developed in an aquarium showed direct evidence of O(2) transport down to a depth of 350 mm of the sediment through a burrow. The 16S rRNA gene-cloning analysis revealed that the betaproteobacterial AOB communities in the sediment surface and the burrow walls were dominated by Nitrosomonas sp. strain Nm143-like sequences, and most of the clones in Nitrospira-like NOB clone libraries of the sediment surface and the burrow walls were related to the Nitrospira marina lineage. Furthermore, we investigated vertical distributions of AOB and NOB in the infaunal burrow walls and the bulk sediments by real-time quantitative PCR (Q-PCR) assay. The AOB and Nitrospira-like NOB-specific 16S rRNA gene copy numbers in the burrow walls were comparable with those in the sediment surfaces. These numbers in the burrow wall at a depth of 50 to 55 mm from the surface were, however, higher than those in the bulk sediment at the same depth. The microelectrode measurements showed higher NH(4)(+) consumption activity at the burrow wall than those at the surrounding sediment. This result was consistent with the results of microcosm experiments showing that the consumption rates of NH(4)(+) and total inorganic nitrogen increased with increasing infaunal density in the sediment. These results clearly demonstrated that the infaunal burrows stimulated O(2) transport into the sediment in which otherwise reducing conditions prevailed, resulting in development of high NH(4)(+) consumption capacity. Consequently, the infaunal burrow became an important site for NH(4)(+) consumption in the intertidal sediment.     

Anaerobic ammonia-oxidizing bacteria and related activity in Baltimore inner harbor sediment

The discovery of bacteria capable of anaerobic ammonia oxidation (anammox) has generated interest in understanding the activity, diversity, and distribution of these bacteria in the environment. In this study anammox activity in sediment samples obtained from the Inner Harbor of Baltimore, Md., was detected by (15)N tracer assays. Anammox-specific oligonucleotide primer sets were used to screen a Planctomycetales-specific 16S rRNA gene library generated from sediment DNA preparations, and four new anammox bacterial sequences were identified. Three of these sequences form a cohesive new branch of the anammox group, and the fourth sequence branches separately from this group. Denaturing gradient gel electrophoresis analysis of sediment incubated with anammox-specific media confirmed the presence of the four anammox-related 16S rRNA gene sequences. Evidence for the presence of anammox bacteria in Inner Harbor sediment was also obtained by using an anammox-specific probe in fluorescence in situ hybridization studies. To our knowledge, this is the first report of anammox activity and related bacterial 16S rRNA gene sequences from the Chesapeake Bay basin area, and the results suggest that this pathway plays an important role in the nitrogen cycle of this estuarine environment. Furthermore, the presence of these bacteria and their activity in sediment strengthen the contention that anammox-related Plactomycetales are globally distributed.     

Abundance and community structure of ammonia-oxidizing microorganisms in reservoir sediment and adjacent soils

Ammonia oxidation is an important process for global nitrogen cycling. Both ammonia-oxidizing bacteria (AOB) and archaea (AOA) can be the important players in nitrification process. However, their relative contribution to nitrification remains controversial. This study investigated the abundance and community structure of AOA and AOB in sediment of Miyun Reservoir and adjacent soils. Quantitative PCR assays indicated that the highest AOA abundance occurred in unplanted riparian soil, followed by reservoir sediment, reed-planted riparian soil and agricultural soil. The AOB community size in agricultural soil was much larger than that in the other habitats. Large variations in the structures of AOA and AOB were also observed among the different habitats. The abundance of Nitrosospira-like AOB species were detected in the agricultural soil and reservoir sediment. Pearson’s correlation analysis showed the AOB diversity had positive significant correlations with pH and total nitrogen, while the AOA diversity might be negatively affected by nitrate nitrogen and ammonia nitrogen. This work could add new insights towards nitrification in aquatic and terrestrial ecosystems.     

Changes in macroinvertebrate community structure and function along a

Aquatic macroinvertebrate communities were sampled between 1994 and 1996 at 13 sites downstream of phosphorus (P)-enriched canal inflows in a northern Everglades marsh to determine the effects of nutrient enrichment on community structure and function. Sampling was performed using sweep nets and Hester–Dendy (HD) samplers. Data were analyzed to assess changes in taxa richness and diversity, species composition, and functional group composition along the gradient. Environmental conditions at each site were characterized to interpret spatial changes in these metrics. Mean water-column total P (TP) increased from 10g l^minus;1at sites in the marsh interior to as high as 160g l^minus;1at sites closest to the canal. Vegetation and habitat composition changed dramatically along the gradient, with sawgrass and slough-wet prairie habitats accounting for most vegetative cover in the interior and cattail accounting for nearly 100%of the cover near the canal. These differences in TP concentrations and vegetation were used to classify sites as reference, enriched, and highly enriched. Daytime dissolved oxygen (DO) concentrations averaged 3mg l^minus;1at reference sites as compared with concentrations 2mg l^minus;1at enriched and highly enriched sites. Total macroinvertebrate densities were significantly higher in sweep samples and significantly lower in HD samples from highly enriched sites as compared with the reference condition. Taxa richness and diversity in sweep samples did not change significantly along the gradient, but declined with enrichment on the HD samplers. Insects were the dominant organisms at all sites, but declined in percent abundance with enrichment in sweep samples due to decreases in dipterans, trichopterans and odonates and an increase in oligochaetes. Changes in major invertebrate classes were less pronounced on HD samplers, although amphipods showed significant declines with enrichment. Principal components analysis revealed a clear distinction in taxonomic composition between reference sites and both enriched and highly enriched sites for sweep samples as common chironomid taxa at reference sites declined with enrichment while pollution-tolerant chironomid and oligochaete taxa increased. A similar, but less dramatic trend was found for HD samples, with selected amphipod, chironomid, and gastropod taxa declining with enrichment and pollution-tolerant taxa reaching peak abundance at enriched sites. The functional composition in sweep samples showed modest changes with enrichment, including a shift in dominance from epibenthic collector–gatherers/deposit feeders, which were predominantly chironomids, to subsurface taxa, which were predominantly oligochaetes. Shifts in invertebrate functional composition on HD samplers with enrichment were attributable to declines in the dominance of shredders and collector-filterer/suspension-feeders. Portions of the Everglades exposed to P-enriched runoff are showing characteristic shifts in macroinvertebrate taxonomic composition related to eutrophication. This shift has occurred without a change in species diversity and with an increase in total invertebrate abundance indicative of an overall increase in marsh productivity. The transition from an oligotrophic to eutrophic community signals a decline in the biological integrity of the Everglades ecosystem in response to P enrichment.     

Virioplankton community structure along a salinity gradient in a solar saltern

The virioplankton community structure along a salinity gradient from near seawater (40 per thousand ) to saturated sodium chloride brine (370 per thousand ) in a solar saltern was investigated by pulsed-field gel electrophoresis. Viral populations with genome sizes varying from 10 kb to 533 kb were detected. The viral community structure changed along the salinity gradient. Cluster analysis of the viral genome-banding pattern resulted in two main clusters. The virioplankton diversity within the samples with salinity from 40 per thousand to 150 per thousand was on the same cluster of a cladogram. The other group consisted of virioplankton from samples with salinity above 220 per thousand. The virioplankton diversity in the different samples was calculated using the Shannon index. The diversity index demonstrated an increase in diversity in the samples along the gradient from 40 per thousand to 150 per thousand salinity, followed by a decrease in the diversity index along the rest of the salinity gradient. These results demonstrate how viral diversity changes from habitats that are considered one of the most common (seawater) to habitats that are extreme in salt concentrations (saturated sodium brine). The diversity index was highest in the environments that lie in between the most extreme and the most common.     

Microbial community structures in anoxic freshwater lake sediment along a metal contamination gradient

Contamination, such as by heavy metals, has frequently been implicated in altering microbial community structure. However, this association has not been extensively studied for anaerobic communities, or in freshwater lake sediments. We investigated microbial community structure in the metal-contaminated anoxic sediments of a eutrophic lake that were impacted over the course of 80 years by nearby zinc-smelting activities. Microbial community structure was inferred for bacterial, archaeal and eukaryotic populations by evaluating terminal restriction fragment length polymorphism (TRFLP) patterns in near-surface sediments collected in triplicate from five areas of the lake that had differing levels of metal contamination. The majority of the fragments in the bacterial and eukaryotic profiles showed no evidence of variation in association with metal contamination levels, and diversity revealed by these profiles remained consistent even as metal concentrations varied from 3000 to 27 000 mg kg⁻¹ total Zn, 0.125 to 11.2 μ pore water Zn and 0.023 to 5.40 μ pore water As. Although most archaeal fragments also showed no evidence of variation, the prevalence of a fragment associated with mesophilic Crenarchaeota showed significant positive correlation with total Zn concentrations. This Crenarchaeota fragment dominated the archaeal TRFLP profiles, representing between 35% and 79% of the total measured peak areas. Lake DePue 16S rRNA gene sequences corresponding to this TRFLP fragment clustered with anaerobic and soil mesophilic Crenarchaeota sequences. Although Crenarchaeota have been associated with metal-contaminated groundwater and soils, this is a first report (to our knowledge) documenting potential increased prevalence of Crenarchaeota associated with elevated levels of metal contamination.     

不同海拔缓步动物群落结构的比较

为研究海拔对缓步动物群落结构的影响,对地处秦岭北坡的南五台山缓步动物群落进行了初步调查研究.调查设置3个样区、45个样方,共采集缓步动物919个,个体密度平均816.89个·m-2,隶属缓步动物门2纲2目3科7属11种.其中Macrobiotus hufelandi和M.harmsworthi共占总采量的92.93%,为优势类群.采用Simpson指数、Shannon-Wiener信息指数、Pielou均匀度指数和修正的Hill指数来计算各生境缓步动物群落结构特点.研究表明,海拔对缓步动物群落结构有一定的影响.随着海拔的下降其物种的个体数量、群落优势类群的数量和优势物种数都呈下降趋势;物种多样性的变化趋势为中海拔地区＞低海拔地区＞高海拔地区,而群落优势度的变化趋势完全相反;不同海拔样区的群落相似性较低.     

Differences in hyporheic-zone microbial community structure along a heavy-metal contamination gradient

The hyporheic zone of a river is nonphotic, has steep chemical and redox gradients, and has a heterotrophic food web based on the consumption of organic carbon entrained from downwelling surface water or from upwelling groundwater. The microbial communities in the hyporheic zone are an important component of these heterotrophic food webs and perform essential functions in lotic ecosystems. Using a suite of methods (denaturing gradient gel electrophoresis, 16S rRNA phylogeny, phospholipid fatty acid analysis, direct microscopic enumeration, and quantitative PCR), we compared the microbial communities inhabiting the hyporheic zone of six different river sites that encompass a wide range of sediment metal loads resulting from large base-metal mining activity in the region. There was no correlation between sediment metal content and the total hyporheic microbial biomass present within each site. However, microbial community structure showed a significant linear relationship with the sediment metal loads. The abundances of four phylogenetic groups (groups I, II, III, and IV) most closely related to alpha-, beta-, and gamma-proteobacteria and the cyanobacteria, respectively, were determined. The sediment metal content gradient was positively correlated with group III abundance and negatively correlated with group II abundance. No correlation was apparent with regard to group I or IV abundance. This is the first documentation of a relationship between fluvially deposited heavy-metal contamination and hyporheic microbial community structure. The information presented here may be useful in predicting long-term effects of heavy-metal contamination in streams and provides a basis for further studies of metal effects on hyporheic microbial communities.     

Zooplankton community structure along a trophic gradient in a canyon-shaped dam reservoir

The zooplankton community was surveyed along the longitudinalaxis of Rimov Reservoir (Czech Republic) on seven occasionsduring the vegetative season of 1996. The dimictic Rimov Reservoirhas a pronounced trophic gradient along its axis. In nearlyall samples, rotifers were dominant by numbers and formed onaverage 60–95% of the total zooplankton (including copepodnauplii). There was a consistent pattern of increasing relativeabundance of rotifers in the upper regions of the reservoircompared with the downstream parts. Very large rotifer populationscould develop in the upper regions, often associated with floodevents, but also coinciding with reduced abundance of crustaceansassociated with stronger wash-out effects and the advent ofturbid conditions. There was a greater similarity between twoadjacent sites in the proportions of crustacean species thanof rotifer species. This is partially due to the greater speciesdiversity of rotifers than of crustaceans. The timing of theseasonal succession of zooplankton species showed a coherentpattern along the whole longitudinal profile. The site-specificzooplankton patchiness seems to be reduced as there was no sitedependence if average data on zooplankton composition from downstreamlacustrine sites were compared.     

Changes in the zooperiphyton structure in a small river along the spatial gradient

A total of 165 taxa have been recorded in the zooperiphyton of the Sestra River, among which larvae of chironomids (40), nematodes (24), and oligochaetes (21) have the highest species richness. The increase in the taxonomic richness of zoocenoses from the river head to its mouth is weakly expressed. The highest diversity of zoocenoses is characteristic for the contact zones of the river water with its tributaries and receiving waters. The discreteness of spatial characteristic of the taxonomic composition of zooperiphyton reflects the heterogeneity and diversity of habitat conditions of invertebrates. In regards to its effect on zoocenoses, anthropogenic pollution can exceed the impact of many environmental factors (including the current velocities) which affect the formation of rheophilic communities in river ecosystems. The dominant complexes of zooperiphyton include all trophic groups of invertebrates, among which the group of detritophages-collectors has the highest taxonomic diversity. The group of phytodetritophages-filterers + collectors mainly includes chironomid larvae of the genus Chironomus, which are associated with strongly polluted zones. Invertebrate filterers, sponges, and bryozoans prevail mainly in zooperiphyton in the lower reaches of the river, which are not subjected to the pollution.     

内蒙古呼伦贝尔草原土壤氨氧化细菌多样性及群落结构

采用聚合酶链式反应-变性梯度凝胶电泳技术及扩增产物序列分析方法,研究了呼伦贝尔5种草地类型(线叶菊草原、贝加尔针茅草原、羊草草原、大针茅草原、克氏针茅草原)土壤氨氧化细菌多样性及群落结构特征.研究表明:不同草地类型间土壤氨氧化细菌群落结构组成差异显著,相似性均低于50%.线叶菊草原土壤氨氧化细菌群落多样性最高,其次是贝加尔针茅草原、羊草草原和克氏针茅草原,大针茅草原最低.5种草地类型土壤氨氧化细菌均以Nitrosospira cluster 3为优势种群,此外还发现有Nitrosospira cluster 1、2、4和Nitrosomonas.线叶菊草原土壤氨氧化细菌群落组成较其他草地类型复杂,而羊草草原和大针茅草原群落组成较简单.经相关性分析,土壤含水量、土壤全氮、有机碳、土壤C/N与土壤氨氧化细菌群落多样性显著正相关(P<0.05).     

Changes in activity and community structure of methane-oxidizing bacteria over the growth period of rice

The activity and community structure of methanotrophs in compartmented microcosms were investigated over the growth period of rice plants. In situ methane oxidation was important only during the vegetative growth phase of the plants and later became negligible. The in situ activity was not directly correlated with methanotrophic cell counts, which increased even after the decrease in in situ activity, possibly due to the presence of both vegetative cells and resting stages. By dividing the microcosms into two soil and two root compartments it was possible to locate methanotrophic growth and activity, which was greatest in the rhizoplane of the rice plants. Molecular analysis by denaturing gradient gel electrophoresis and fluorescent in situ hybridization (FISH) with family-specific probes revealed the presence of both families of methanotrophs in soil and root compartments over the whole season. Changes in community structure were detected only for members of the Methylococcaceae and could be associated only with changes in the genus Methylobacter and not with changes in the dominance of different genera in the family Methylococcaceae. For the family Methylocystaceae stable communities in all compartments for the whole season were observed. FISH analysis revealed evidence of in situ dominance of the Methylocystaceae in all compartments. The numbers of Methylococcaceae cells were relatively high only in the rhizoplane, demonstrating the importance of rice roots for growth and maintenance of methanotrophic diversity in the soil.     

Diversity and phylogenetic community structure of ants along a Costa Rican elevational gradient

The diversity and phylogenetic community structure of many organisms is negatively affected by factors that covary with elevation. On the Pacific slope of the Cordillera Guanacaste within Area de Conservación Guanacaste (ACG) in northwestern Costa Rica we found a negative relationship between elevation and ant diversity on each of three volcanos. This pattern was evident when diversity was measured through molecular operational taxonomic units (MOTU) or by phylogenetic diversity (PD) based on DNA barcodes or a multi‐gene phylogeny. We observed an asymmetrical mid‐elevation peak at approximately 600–800 m and we found high species turnover between sites on the same mountain and among the three mountains. At the highest elevation cloud forest sites we found evidence of significant phylogenetic clustering, the expected result of environmental filtering. The narrow elevational range of each species, coupled with the high diversity at each sampling point, emphasizes that climate change will bring strong changes in the location and composition of biodiversity on these mountains. The structure and composition of the hyperdiverse communities present at any one elevation is extremely vulnerable to a changing climate.