Direct and indirect food web regulation of microbial decomposers in headwater streams

The direct and indirect regulation of primary productivity has been well established in autotrophic‐based ecosystems; however, less is known about the processes affecting decomposers in detrital‐based ecosystems. Because, small headwater, woodland streams are a dominate feature in most ecosystems and are tightly linked to terrestrial detritus, understanding decomposer‐mediated functions in these systems is critical for understanding carbon processes across the landscape. In this light, we conducted a microcosm and mesocosm experiment to test the direct and indirect food web effects on decomposers in small stream ecosystems. The results from the microcosm experiment supported an existing literature, demonstrating that nutrients directly stimulate decomposers and that microbivores directly reduce decomposers. Based on well‐founded food web theory in autotrophic systems, we predicted that fishes from different trophic‐functional guilds would indirectly stimulate decomposers by enhancing dissolved nutrients and by reducing microbivore densities. Our mesocosm experiment partially supported these predictions. Specifically, we found that fishes that consumed mostly terrestrial foods increased decomposers from the bottom–up by enhancing allochthonous nutrient loading into the stream ecosystems. Contrary to our predictions, however, predatory fishes that consume microbivores did not increase decomposers from the top–down. Rather, in streams with the predatory fish species, microbivores increased (rather than decreased) on leaf litter. This may have resulted from an experimental artifact associated with refuge provided by leaf packs. In conclusion, our data demonstrate that decomposers are regulated by similar direct and indirect processes important in autotrophic‐based ecosystems. This provides further evidence that food web processes can regulate leaf decomposition and flux of detrital carbon through ecosystems.     

Direct and indirect effects of predation on tadpole community structure in the Amazon rainforest

Abstract The relationship between the distribution of predators (fish, odonates and water beetles) and prey assemblages (amphibian larvae) was investigated in the tropical rainforest of central Amazonas, Brasil. The anuran community uses a variety of waterbodies for reproduction, ranging from streams and streamside ponds to isolated forest ponds. Predators in this system include fish in streams and streamside ponds, and invertebrates (primarily odonate naiads and beetles) in forest ponds. Tadpole species richness and assemblage structure were related to fish density and species richness. No relationships between tadpole assemblages and abiotic pond characteristics were detected. The presence offish explained much of the variation in both species composition and species richness within and among ponds. Some species of tadpole were consistently found to coexist with high densities of fish. Path analyses suggest that while fish have a strong direct effect on tadpole associations and species richness, they also have an indirect effect through invertebrate predators (odonate larvae and coleopteran beetles). Prey survival-strategies such as palatability and behaviour may explain how tadpole species composition is affected by predators at the community level. These findings suggest that the observed patterns of habitat use by larval anurans may be structured in response to the distribution of key predators (fish) in this system.     

The influence of alfalfa-switchgrass intercropping on microbial community structure and function

The use of nitrogen fertilizer on bioenergy crops such as switchgrass results in increased costs, nitrogen leaching and emissions of N₂O, a potent greenhouse gas. Intercropping with nitrogen-fixing alfalfa has been proposed as an environmentally sustainable alternative, but the effects of synthetic fertilizer versus intercropping on soil microbial community functionality remain uncharacterized. We analysed 24 metagenomes from the upper soil layer of agricultural fields from Prosser, WA over two growing seasons and representing three agricultural practices: unfertilized switchgrass (control), fertilized switchgrass and switchgrass intercropped with alfalfa. The synthetic fertilization and intercropping did not result in major shifts of microbial community taxonomic and functional composition compared with the control plots, but a few significant changes were noted. Most notably, mycorrhizal fungi, ammonia-oxidizing archaea and bacteria increased in abundance with intercropping and fertilization. However, only betaproteobacterial ammonia-oxidizing bacteria abundance in fertilized plots significantly correlated to N₂O emission and companion qPCR data. Collectively, a short period of intercropping elicits minor but significant changes in the soil microbial community toward nitrogen preservation and that intercropping may be a viable alternative to synthetic fertilization.     

The influence of riparian vegetation on macroinvertebrate community structure in four Hong Kong streams

The benthic macroinvertebrate communities of four Hong Kong streams with similar water chemistry but differing riparian conditions were investigated. Differences in chlorophylls and detritus standing stocks reflected the degree of shading by riparian vegetation; Tai Po Kau Forest Stream (TPKFS) and Bride's Pool (BP) had an allochthonous food base while autochthonous energy sources were relatively more important in Lam Tsuen River (LTR) and Pui O Stream (POS). The macrobenthos was dominated by aquatic insects and morphospecies richness (excluding Chironomidac) ranged from 70 (POS) to 94 (TPKFS). Differences in total macroinvertebrate abundance across sites were not related to chlorophylls or detritus.
Highly significant differences in the morphospecies comprising the most numerous taxa at each site were observed, and TPKS and BP were more similar to each other than to the LTR-POS pair with respect to top-ranked taxa. Intraspecific comparisons of the abundance of these taxa revealed significant differences for 23 out of 30 morphospecies. Multiple regression of the abundance of key morphospecies against independent variables (chlorophylls a , b and c , total chlorophyll and detritus) yielded significant best-fit models for all taxa showing intersite differences in abundance. These data can be interpreted as reflecting the influence of riparian vegetation on stream community structure via an effect on food supply. The results were discussed with reference to the applicability of the River Continuum Concept in the tropics.     

Mercury and other heavy metals influence bacterial community structure in contaminated Tennessee streams

High concentrations of uranium, inorganic mercury [Hg(II)], and methylmercury (MeHg) have been detected in streams located in the Department of Energy reservation in Oak Ridge, TN. To determine the potential effects of the surface water contamination on the microbial community composition, surface stream sediments were collected 7 times during the year, from 5 contaminated locations and 1 control stream. Fifty-nine samples were analyzed for bacterial community composition and geochemistry. Community characterization was based on GS 454 FLX pyrosequencing with 235 Mb of 16S rRNA gene sequence targeting the V4 region. Sorting and filtering of the raw reads resulted in 588,699 high-quality sequences with lengths of >200 bp. The bacterial community consisted of 23 phyla, including Proteobacteria (ranging from 22.9 to 58.5% per sample), Cyanobacteria (0.2 to 32.0%), Acidobacteria (1.6 to 30.6%), Verrucomicrobia (3.4 to 31.0%), and unclassified bacteria. Redundancy analysis indicated no significant differences in the bacterial community structure between midchannel and near-bank samples. Significant correlations were found between the bacterial community and seasonal as well as geochemical factors. Furthermore, several community members within the Proteobacteria group that includes sulfate-reducing bacteria and within the Verrucomicrobia group appeared to be associated positively with Hg and MeHg. This study is the first to indicate an influence of MeHg on the in situ microbial community and suggests possible roles of these bacteria in the Hg/MeHg cycle.     

氮添加土壤微生物群落结构影响微生物碳利用效率

尽管近年来中国氮(N)沉降水平逐渐趋于稳定,但中国东南地区N沉降相比于其他地区仍处于较高水平。N沉降对陆地生态系统碳循环过程的影响不容忽视。微生物碳利用效率(CUE)是指微生物将吸收的碳转化为生物量碳的效率,高微生物CUE意味着高土壤有机碳存储潜力。因此,探究N沉降背景下微生物CUE的变化将有助于进一步认识陆地生态系统土壤碳存储的变化。然而,目前关于N沉降下微生物群落结构的变化如何影响微生物CUE鲜有报道。在福建省泉州市戴云山国家级自然保护区的罗浮栲林通过N添加模拟N沉降。实验共包括三个N添加处理：对照(CT,+0 kg hm^-2 a^-1)、低氮(LN,+40 kg hm^-2 a^-1)和高氮(HN,+80 kg hm^-2 a^-1)。测定不同处理土壤基本理化性质、微生物生物量、酶活性和CUE,并使用高通量测序对微生物群落结构和多样性进行测定。结果表明,N添加显著影响微生物CUE,随着N添加水平的增加,CUE逐渐增加;相反,土壤pH、可提取有机碳(EOC)和微...     

The influence of riparian vegetation on macroinvertebrate community structure and functional organization in six new Guinea streams

Information on the ecology of New Guinea streams is meagre, and data are needed on the trophic basis of aquatic production in rivers such as the Sepik in Papua New Guinea which have low fish yields. This study investigates the relationship between riparian shading (from savanna grassland to primary rainforest), algal and detrital food, and macroinvertebrate abundance and community structure in 6 Sepik River tributary streams. A particular aim was to elucidate macroinvertebrate community responses to changes in riparian conditions. All streams supported diverse benthic communities, but morphospecies richness (overall total 64) was less than in streams on the tropical Asian mainland; population densities of benthic invertebrates, by contrast, were similar to those recorded elsewhere. Low diversity could reflect limited taxonomic penetration, but may result from the absence of major groups (Plecoptera, Heptageniidae, Ephemerellidae, Psephenidae, Megaloptera, etc.) which occur on the Asian mainland. Population densities of all 19 of the most abundant macroinvertebrate taxa varied significantly among the 6 study streams, but community composition in each was broadly similar with dominance by Baetidae and (in order of decreasing importance), Leptophlebiidae, Orthocladiinae, Elmidae and Hydropsychidae. Principal components analysis (PCA) undertaken on counts of abundant macroinvertebrate taxa clearly separated samples taken in two streams from the rest. Both streams contained high detrital standing stocks and one was completely shaded by rainforest. Stepwise multiple-regression analysis indicated that population densities of the majority of abundant taxa (11 out of 19) across streams (10 samples per stream; n = 60) were influenced by algae and/or detritus, although standing stocks of these variables were not clearly related to riparian conditions. When regression analysis was repeated on mean counts of taxa per stream (dependent variables) versus features of each stream as a whole (thus n = 6), % shading and detritus were the independent variables yielding significant regression models most frequently, but pH, total-nitrogen loads and algae were also significant predictors of faunal abundance. Further regression analysis, undertaken separately on samples (n = 10) from each stream, confirmed the ability of algae and detritus to account for significant portions of the variance in macroinvertebrate abundance, but the significance of these variables varied among streams with the consequence that responses of individual taxa to algae or detritus was site-specific.Community functional organization — revealed by investigation of macroinvertebrate functional feeding groups (FFGs) — was rather conservative, and streams were codominated by collector-gatherers (mean across 6 streams = 43%) and grazers (36%), followed by filter-feeders (15%) and predators (7%). The shredder FFG was species-poor and comprised only 0.4% of total macroinvertebrate populations; shredders did not exceed 2% of benthic populations in any stream. PCA of FFG abundance data was characterized by poor separation among streams, although there was some evidence of clustering of samples from unshaded sites. The first 2 PCA axes accounted for 84% of the variation in the data suggesting that the poor separation resulted from the general similarity of FFG representation among streams. Although stepwise multiple-regression analysis indicated that algae and detritus accounted for significant proportions of the variations in population density and relative abundance of some FFGs, the response of community functional organization to changes in riparian conditions and algal and detrital food base was weak — unlike the deterministic responses that may be typical of north-temperate streams.     

Urbanisation and earthquake disturbance influence microbial nutrient limitation in streams

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The influence of soluble microbial products on microbial community composition: hypothesis of microbial community succession

Soluble microbial products (SMP) are organic compounds produced by activated sludge microorganisms as they degrade substrates. They include by-products of microbial activity, death and lysis. The available literature does not reveal how SMP influence microbial community composition. In this regard, we microscopically studied changes in composition of microbial communities, especially protozoa and metazoa, under the influence of increased as well as reduced levels of SMP. The presence of SMP at high level significantly caused changes in microbial community composition. Microbial species shifted from attached ciliates (12-175 microm) to free-swimming and crawling ciliates (35-330 microm) and then invertebrates, which included rotifers (0.2-1 mm) and nematodes (1-50 mm). The shift of small-size microorganisms to large ones was observed as one of the most significant influences of SMP. Attached ciliates reappeared when we removed the SMP that had accumulated in the bioreactors - we have called this as the resurrection phenomenon of microorganisms. Such rapid changes in microbial community composition were not observed in the experiment with low concentration of SMP. Overall, the results suggest that accumulation of SMP is one of the intrinsic regulatory mechanisms that control viability and dormancy of microbial communities in activated sludge.     

Heterotrophic flagellate biodiversity and community structure in freshwater streams

The species diversity and community structure of heterotrophic flagellates in watercourses from different geographical regions were investigated. Forty-one species have been identified. The species diversity of cercomonads, kinetoplastids, choanoflagellates, and flagellates is the highest. Bodo saltans, B. designis and Goniomonas truncata are the most common species. Planktonic communities in different streams are most similar in terms of species composition. The highest similarity within benthic cenoses was noted between geographically distant communities. Communities of heterotrophic flagellates seem to be highly heterogenous systems; species distribution depends mainly on the type of habitat and not on geographical factors.     

Microenvironments and microbial community structure in sediments

The aim of this study was to explore the potential of a combined chemical and microbiological approach as part of a study of organic carbon oxidation processes in sediments. An assessment of microbiological diversity using molecular techniques was carried out in combination with high resolution chemical measurements at the sediment-water interface of a coastal lagoon affected by eutrophication in autumn 2000. There was a 0.2 mm overlap between the O2 and H2S profiles. pH showed a maximum just above the sediment-water interface coinciding with an oxygen maximum, suggesting photosynthetic activity, and a minimum coinciding with the O2-H2S interface. The redox potential was high in bottom water and surface sediment, reflecting the presence of oxygen and oxides, and reached low values after a step-wise decrease at -18 mm. Reduction of Fe occurred within the biofilm at the O2-H2S interface and was mostly due to reduction by H2S. The elevated concentrations of dissolved Mn in the oxic water may have been caused either by in situ production within organic aggregates or lateral water flow from sites nearby at which Mn2+ diffuses out of the sediment. Sequences related to sulphur chemolitotrophs were retrieved from the biofilm samples, which is consistent with the small overlap between O2 and H2S observed in this biofilm. Although the resolution of techniques used was different, sequencing results were consistent with chemical data in delineating the same horizons according to redox, pH or ecological properties.     

青藏高原湖泊沉积物中有机碳组分构成及其对微生物群落结构的影响

【目的】探究湖泊沉积物中有机碳组分构成及其对湖泊微生物群落结构的影响。【方法】本研究采集了青藏高原29个湖泊共81个沉积物样品,通过硫酸水解法分析样品中易降解和难降解有机碳含量及其与环境变量之间的相关性;同时使用高通量测序技术分析样品中原核微生物和真菌群落的多样性和组成及其与易降解和难降解有机碳含量的相关关系。【结果】本研究的青藏高原湖泊沉积物中易降解有机碳Ⅰ(labile organic carbon Ⅰ, LOCⅠ)、易降解有机碳Ⅱ(labile organic carbon Ⅱ, LOCⅡ)和难降解有机碳(recalcitrant organic carbon, ROC)的含量分别为0.03–29.62 mg/g、0.02–23.38 mg/g和0.64–75.72 mg/g,ROC是沉积物有机碳的主要组分(占比为54.97%±19.50%)。LOCⅠ含量与海拔、总氮、总磷、钙离子、活性钙和活性铁含量显著相关(P<0.05);LOCⅡ含量与总氮、钙离子和活性钙含量显著相关;而ROC含量与海拔、总氮、总磷、钙离子和活性钙含量显著相关。其中,钙离子和活性钙的浓度与3种有机碳组分...     

Direct and indirect influence of sulfur availability on phytoplankton evolutionary trajectories

The sulfate facilitation hypothesis suggests that changes in ocean sulfate concentration influenced the rise to dominance of phytoplankton species of the red lineage. The mechanistic reasons for this phenomenon are not yet understood. We started to address this question by investigating the differences in S utilization by algae of the green and red lineages and in cyanobacteria cultured in the presence of either 5 mmol · L^?1 (approximately equivalent to Paleozoic ocean concentrations) or 30 mmol · L^?1 (corresponding to post‐Mesozoic/extant concentrations) sulfate. The activities of the main enzymes involved in SO₄^2? assimilation changed in response to changes in growth sulfate concentration. ATP sulfurylase showed different kinetics in the various taxa, with an especially odd behavior for the dinoflagellate. Sulfate availability had a modest effect on cell organic composition. Species‐specific differences in the use of some elements were instead obvious in algae grown in the presence of different sulfate concentrations, overall confirming that algae of the red lineage do better at high sulfate than algae of the green lineage. The increase in sulfate concentration may thus have had an impact on phytoplankton radiation both through changes in their enzymatic machinery and through indirect repercussion on elemental usage.     

Soil and plant effects on microbial community structure

We investigated the effects of two different plant species (corn and soybean) and three different soil types on microbial community structure in the rhizosphere. Our working hypothesis was that the rhizosphere effect would be strongest on fast-growing aerobic heterotrophs, while there would be little or no rhizosphere effect on oligotrophic and other slow-growing microorganisms. Culturable bacteria and fungi had larger population densities in the rhizosphere than in bulk soil. Communities were characterized by soil fatty acid analysis and by substrate utilization assays for bacteria and fungi. Fatty acid analysis revealed a very strong soil effect but little plant effect on the microbial community, indicating that the overall microbial community structure was not affected by the rhizosphere. There was a strong rhizosphere effect detected by the substrate utilization assay for fast-growing aerobic heterotrophic bacterial community structure, with soil controls and rhizosphere samples clearly distinguished from each other. There was a much weaker rhizosphere effect on fungal communities than on bacterial communities as measured by the substrate utilization assays. At this coarse level of community analysis, the rhizosphere microbial community was impacted most by soil effects, and the rhizosphere only affected a small portion of the total bacteria.     

Direct and indirect effects of invasions of predators on a multiple-species community

A Lotka-Volterra system for a multiple species community with two trophic levels is analyzed to illustrate how community structure is reorganized upon invasions of predators. The lower trophic level is assumed to consist of interfering competing species, some of which are preferentially consumed by invading predators. Effects of invading predators on the lower trophic level are investigated in terms of predator-mediated coexistence and predator-induced instability. Competitive interactions between species in the lower trophic level result in indirect mutualism or indirect competition between predators depending on which competitors are preyed upon.     

Top-down and bottom-up processes in grassland and forested streams

The influence of predatory fish on the structure of stream food webs may be altered by the presence of forest canopy cover, and consequent differences in allochthonous inputs and primary production. Eight sites containing introduced brown trout (Salmo trutta) and eight sites that did not were sampled in the Cass region, South Island, New Zealand. For each predator category, half the sites were located in southern beech (Nothofagus) forest patches (range of canopy cover, 65–90%) and the other half were in tussock grassland. Food resources used by two dominant herbivores-detritivores were assessed using stable isotopes. ¹³C/¹²C ratios were obtained for coarse particulate organic matter (CPOM), fine particulate organic matter (FPOM), algal dominated biofilm from rocks, and larvae of Deleatidium (Ephemeroptera) and Olinga (Trichoptera). Total abundance and biomass of macroinvertebrates did not differ between streams with and without trout, but were significantly higher at grassland sites than forested sites. However, taxon richness and species composition differed substantially between trout and no-trout sites, irrespective of whether streams were located in forest or not. Trout streams typically contained more taxa, had low biomass of predatory invertebrates and large shredders, but a high proportion of consumers with cases or shells. The standing stock of CPOM was higher at forested sites, but there was less FPOM and more algae at sites with trout, regardless of the presence or absence of forest cover. The stable carbon isotope range for biofilm on rocks was broad and encompassed the narrow CPOM and FPOM ranges. At trout sites, carbon isotope ratios of Deleatidium, the most abundant invertebrate primary consumer, were closely related to biofilm values, but no relationship was found at no-trout sites where algal biomass was much lower. These results support a role for both bottom-up and top-down processes in controlling the structure of the stream communities studied, but indicate that predatory fish and forest cover had largely independent effects.     

Effects of deforestation on fish community structure in Ecuadorian Amazon streams

SUMMARY 1. There is little information on the impacts of deforestation on the fish fauna in neotropical streams, and on parameters influencing species diversity and community structure of fish. We analysed these aspects in 12 stream sites in the Ecuadorian Amazon. The stream sites represented a large gradient in canopy cover and were located in an area of fragmented forest. While some streams had been deforested, they had not suffered gross degradation of the habitat.
2. The species richness of stream fish was not related to deforestation. Local fish diversity (Fisher's Alpha) was positively related to the surface area of stream pools (m²). Beta diversity was higher among forested than deforested sites, indicating greater heterogeneity in species composition among forested than deforested sites. The percentage of rare species was positively correlated with canopy cover.
3. Total fish density increased with deforestation, and the fish community changed from dominance by omnivorous and insectivorous Characiformes at forested sites to dominance of periphyton-feeding loricariids at deforested sites.
4. Multidimensional statistical analysis of fish community structure showed that six environmental variables (the area of stream bottom covered by leaves, relative pool area, particulate organic matter, mean depth, conductivity and suspended solids) were related to the ordination axes. The presence of leaves, which was strongly correlated to canopy cover, was the variable most closely related to fish community structure, while relative pool area was the second strongest variable. Thus, fish community structure was strongly affected by deforestation.     

高寒森林溪流微生物群落结构的季节性变化

高寒森林溪流不仅是区域河流的源头,而且是联系陆地与水域的生态纽带。微生物活动可能成为控制溪流生态系统过程的关键因子,但其结构与动态过程缺乏必要关注。因此,结合同步温度动态监测,采用实时荧光定量PCR和DGGE技术,在2014年到2015年冻融季节和生长季节关键时期对比研究了川西高寒森林溪流和森林林下土壤中微生物群落的动态特征。研究结果发现,高寒森林溪流具有较低的真菌和细菌群落丰度;与森林土壤相同,溪流在冻融季节表现出相对生长季节更高的真菌/细菌比,而且从冻融季节到生长季节,溪流微生物丰度动态也表现出明显的季节性变化特征。与森林土壤不同的是,溪流中细菌和真菌的丰度及其Shannon-Wiener多样性指数的最高值均出现在生长季节而不是冬季冻融季节,并且溪流中细菌丰度在季节性变化的不同时期具有显著差异(P0.05)。此外,森林土壤细菌类群以芽孢杆菌属(Bacillus sp.)比例相对较高,真菌类群则以格孢菌属(Pleosporales sp.)、曲霉属(Aspergillus sp.)和其他一些子囊菌门(Ascomycota)的类群为优势;而溪流细菌类群以红球菌属(Rhodococcus sp.)为主,真菌类群则以曲霉属和空团菌属(Cenococcum sp.)为主。同时,季节性变化中温度、p H、水溶性有机碳和溶解氧等环境因子可显著影响溪流微生物群落结构及其组成,这些环境因子在高寒森林溪流微生物群落的季节性变化过程中具有重要的作用。