Bacterial interactions in the rhizosphere of seagrass communities in shallow coastal lagoons

Rooted phanerogam communities in the shallow intertidal and subtidal coastal zone represent productive and healthy ecosystems. Inorganic nutrients are assimilated into seagrass biomass. Much of the organic matter resulting from moribund seagrass is rapidly mineralized, principally by bacteria. The microbial community of the rhizosphere is also highly active due to the supply of organic matter released during photosynthesis. This active sediment community plays an important role through carbon, nitrogen and phosphorous cycling in maintaining the stability and productivity of seagrass meadows. Over the last two decades, however, seagrass meadows in European coastal areas have declined due to increasing pollution. As eutrophication advances a trasition occurs from rooted phanerogram dominated communities to planktonic algal blooms and/or cyanobacterial blooms. Such changes represent the decline of a stable, high biodiversity habitat to an unstable one dominated by a few species. These changes of community structure can occur rapidly once the internal nutrient and organic matter control cycles are exceeded. A field investigation was undertaken to establish the spatial distribution of bacterial populations of Zostera noltii colonized and uncolonized sediment in the Bassin d'Arcachon, France. Bacteria were enumerated using both plate count and MPN techniques for different functional groups as well as determining the total bacterial populations present. Nitrogen fixation, ammonification, sulphate reduction rates, as well as alkaline phosphatase activity were also determined. Colonization of the Z. noltii roots and rhizomes was studied by light and scanning electron microscopy. Results confirmed that higher bacterial populations were present in the rhizosphere of Z. noltii compared to uncolonized sediments. Furthermore, electron microscopy identified the rhizome as the main site of colonization for a diverse range of morphological groups of bacteria. Sulphate reducing bacteria were identified as the key group of bacteria involved in N-fixation in the rhizosphere of Z. noltii. The data will be discussed in relation to the role played by the rhizosphere microflora in supplying and mobilising nutrients in Z. noltii.     

Community dominance patterns, not colonizer genetic diversity, drive colonization success in a test using grassland species

Successful colonization and/or invasion depend on characteristics of the invaded community and of the colonizer itself. Although many studies have documented a negative relationship between invasibility and biodiversity, the importance of community evenness is rarely examined and thus poorly understood. However, colonizer characteristics, including population genetic diversity, can also be important determinants of colonization success. We conducted a greenhouse experiment to assess the relative importance of community evenness and colonizer population genetic diversity using the weed Arabidopsis thaliana. We added seeds of A. thaliana (varying genetic diversity while keeping propagule pressure constant) to four types of constructed plant communities: those dominated by legumes, grasses or forbs, or with equal abundances of all three functional groups. We selected community members from a large pool of species to avoid the confounding effects of species identity. We also assessed the success of multiple seedbank colonizers to assess generality in the effects of our evenness treatments. Equal-abundance communities were no better at suppressing colonization than communities dominated by a single functional group. Forb-dominated communities suppressed A. thaliana colonization better than grass-dominated communities and suppressed seedbank colonizers better than legume-dominated communities. Equal-abundance communities were similar to forb-dominated ones in their eventual composition and in their invasibility, suggesting that forbs drove colonizer suppression in that treatment rather than high evenness itself. Most of our forbs grew quickly, yielding productive forb-dominated communities; this points to the importance of growth and colonization phenology in our system. A. thaliana genetic diversity did not affect colonization success, perhaps because strong interspecific competition substantially limited A. thaliana seedling emergence.     

An approach to analysis of colonization dynamics in community functioning of protozoa for bioassessment of marine pollution

Biological trait analysis is a powerful tool to summarize the spatial/temporal patterns of community functioning and ecosystem process at taxon-free resolutions. To identify the optimal colonization period with high homogeneity in functional patterns of protozoa for bioassessment, 1-month baseline colonization survey was conducted in coastal waters of the Yellow Sea. A fuzzy-coding functional trait system was used to summarize the functional structure of protozoan communities during the colonization process. The functional patterns showed a low homogeneity during the early stage (3–7 days), followed by a stable stage (10–14 days) with high homogeneity, and the last stage (21–28 days) with high heterogeneity. The functional richness showed a low variability, while the functional evenness and divergence generally showed a decreasing trend during the whole colonization process. Furthermore, the functional dispersion and RaoQ indices generally leveled off only during the stable stage. These results suggest that it is necessary to determine the optimal exposure time period with high homogeneity of community functioning for bioassessment using protozoan colonization in marine ecosystems.     

Protozoan communities of the Flint River-Lake Blackshear ecosystem (Georgia,USA)

Freshwater protozoa are poorly characterized in river ecosystems. We report here the richness of the protozoan biotas in relation to environmental gradients from an ecosystematic survey of a large, coastal plain river. Communities were collected from natural and artificial substrates concurrent with water chemistry analysis at 11 sites along the Flint River and Lake Blackshear impoundment. Community similarity, the distribution of collected taxa in functional feeding groups, and the relation of communities to environmental gradients were evaluated. Two principal compenents determined from water chemistry data showed important downstream gradients of decreasing water hardness and increasing nutrient levels. Taxonomic richness was high; 200 to 450 taxa were collected depending on season and collecting technique. Artificial substrates provided the richest collections. Bactivorous species were the vast majority of all taxa collected. Community composition showed an orderly transition from upstream to downstream, and photosynthetic forms were enhanced at nutrient enriched sites. Communities were strongly influenced by increasing nutrient levels. Protozoan community analysis showed that microbial community composition reflects human influences on river ecosystems. Since microbial species exploit detrital resources and respond sensitively to human influences, they can provide important information regarding ecosystem conditions.     

Phylogenetic similarity and structure of Agaricomycotina communities across a forested landscape

The Agaricomycotina are a phylogenetically diverse group of fungi that includes both saprotrophic and mycorrhizal species, and that form species – rich communities in forest ecosystems. Most species are infrequently observed, and this hampers assessment of the role that environmental heterogeneity plays in determining local community composition and in driving β‐diversity. We used a combination of phenetic (TRFLP) and phylogenetic approaches [Unifrac and Net Relatedness Index (NRI)] to examine the compositional and phylogenetic similarity of Agaricomycotina communities in forest floor and surface soil of three widely distributed temperate upland forest ecosystems (one, xeric oak – dominated and two, mesic sugar maple dominated). Generally, forest floor and soil communities had similar phylogenetic diversity, but there was little overlap of species or evolutionary lineages between these two horizons. Forest floor communities were dominated by saprotrophic species, and were compositionally and phylogenetically similar in all three ecosystems. Mycorrhizal species represented 30% to 90% of soil community diversity, and these communities differed compositionally and phylogenetically between ecosystems. Estimates of NRI revealed significant phylogenetic clustering in both the forest floor and soil communities of only the xeric oak‐dominated forest ecosystem, and may indicate that this ecosystem acts as a habitat filter. Our results suggest that environmental heterogeneity strongly influences the phylogenetic β‐diversity of soil inhabiting Agaricomycotina communities, but has only a small influence on forest floor β‐diversity. Moreover, our results suggest that the strength of community assembly processes, such as habitat filtering, may differ between temperate forest ecosystems.     

高寒草甸不同草地类型功能群多样性及组成对植物群落生产力的影响

对不同类型草地功能群多样性和组成与植物群落生产力之间的关系进行了探讨。结果表明：(1)在矮嵩草(Kobresia humlis)草甸和金露梅(Potentilla froticosa)灌丛中,豆科植物的作用比较明显,而其他功能群植物的作用较弱。(2)在藏嵩草(Kobresia tibetica)沼泽化草甸和小嵩草(K．pygmaca)草甸中,虽然杂类草、C3植物和莎草科植物功能群的生产力占群落初级生产力的比例较大,但二者在统计上没有显著性差异,这表明群落生产力除受物种多样性的影响外,也受物种本身特征和环境资源的影响,更主要的是受到功能群内物种密度和均匀度的影响,即功能群组成比功能群多样性更能说明对生态系统过程的影响。(3)不同类型草地群落植物功能群盖度与群落初级生产力呈显著的线性相关。(4)不同类型草地群落生产力与功能群内物种数的变化均表现为单峰曲线关系,即功能群内物种数处于中间水平时,群落生产力最高。     

Identifying functional species pool of planktonic protozoa for discriminating water quality status in marine ecosystems

It is cost-effective protocol to identify a functional species pool for marine bioassessment by removing redundant species from a raw dataset. The feasibility of functional species pool for discriminating water quality status was studied based on a dataset of 120 samples of ciliated protozoa. From the full 60-species dataset of the whole ciliate communities, a 35-species subset was identified as a functional species pool, the species number, abundance and biodiversity indices of which were significantly correlated with those of the full species dataset. The spatial pattern of the subset was significantly related to the changes in nutrients soluble reactive phosphates (SRP), nitrate/nitrite nitrogen (NO₃-N/NO₂-N) and ammonium nitrogen (NH₄-N). Four indices of the taxonomic diversity (Δ), taxonomic distinctness (Δ*), average in taxonomic distinctness (Δ⁺) and the variation in taxonomic distinctness (Λ⁺) based on this small species pool were significantly correlated with the changes of nutrients NO₃-N and/or (NH₄-N). The paired indices Δ⁺ and Λ⁺ showed a clear decreasing trend of departure from the expected taxonomic pattern. These findings suggest that the 35-species functional species subset may be used as a feasible functional surrogate of ciliated protozoan assemblages for community-based bioassessment in marine ecosystems.     

Temporal and spatial constraints on community assembly during microbial colonization of wood in seawater

Wood falls on the ocean floor form chemosynthetic ecosystems that remain poorly studied compared with features such as hydrothermal vents or whale falls. In particular, the microbes forming the base of this unique ecosystem are not well characterized and the ecology of communities is not known. Here we use wood as a model to study microorganisms that establish and maintain a chemosynthetic ecosystem. We conducted both aquaria and in situ deep-sea experiments to test how different environmental constraints structure the assembly of bacterial, archaeal and fungal communities. We also measured changes in wood lipid concentrations and monitored sulfide production as a way to detect potential microbial activity. We show that wood falls are dynamic ecosystems with high spatial and temporal community turnover, and that the patterns of microbial colonization change depending on the scale of observation. The most illustrative example was the difference observed between pine and oak wood community dynamics. In pine, communities changed spatially, with strong differences in community composition between wood microhabitats, whereas in oak, communities changed more significantly with time of incubation. Changes in community assembly were reflected by changes in phylogenetic diversity that could be interpreted as shifts between assemblies ruled by species sorting to assemblies structured by competitive exclusion. These ecological interactions followed the dynamics of the potential microbial metabolisms accompanying wood degradation in the sea. Our work showed that wood is a good model for creating and manipulating chemosynthetic ecosystems in the laboratory, and attracting not only typical chemosynthetic microbes but also emblematic macrofaunal species.     

Functional traits,spatial patterns and species associations: what is their combined role in the assembly of wetland plant communities?

Studies of community assembly focus on finding rules that predict which species can become member of a plant community. Within a community, species can be categorized in two ways: functional groups classify species according to their functional traits, whereas generalized guilds group species based on their (co-)occurrence, spatial distribution and abundance patterns. This study searches for community assembly rules by testing for coherence among functional groups and generalized guilds, as well as for correlations between the individual functional traits and assembly features, in two wetland plant communities in South Africa. The classifications of functional groups and generalized guilds were not consistent. However, rhizome internode length was related to fine-scale spatial pattern, suggesting that in systems dominated by clonal species (including wetlands, where recruitment sites are strongly limited) community assembly may be strongly linked to colonization ability. Functional groups do not predict guilds in wetland plant communities, precluding their use as the basis for assembly rules. However, an explicit consideration of clonal strategies and their effect on species’ spatial patterns appears to be important for understanding community assembly in systems dominated by clonal plants.     

Subsidies mediate interactions between communities across space

Most spatial ecology focuses on how species dispersal affects community dynamics and coexistence. Ecosystems, however, are also commonly connected by flows of resources. We experimentally tested how neighbouring communities indirectly influence each other in absence of dispersal, via resource exchanges. Using two‐patch microcosm meta‐ecosystems, we manipulated community composition and dynamics, by varying separately species key functional traits (autotroph versus heterotroph species and size of consumer species) and trophic structure of aquatic communities (species growing alone or in presence of competitors or predators). We then analysed the effects of species functional traits and trophic structure on communities connected through spatial subsidies in the absence of actual dispersal. Both functional traits and trophic structure strongly affected dynamics across neighbouring communities. Heterotroph communities connected to autotroph neighbours developed better than with heterotroph neighbours, such that coexistence of competitors was determined by the functional traits of the neighbouring community. Densities in autotroph communities were also strikingly higher when receiving subsidies from heterotroph communities compared to their own subsidies when grown in isolated ecosystems. In contrast, communities connected to predator‐dominated ecosystems collapsed, without any direct contact with the predators. Our results demonstrate that because community composition and structure modify the distribution of biomass within a community, they may also affect communities connected through subsidies through quantitative and qualitative changes of detritus flows. This stresses that ecosystem management should account for such interdependencies mediated by spatial subsidies, given that local community alterations cascade across space onto other ecosystems even if species dispersal is completely absent.     

Seasonal variations in colonization dynamics of periphytic protozoa in coastal waters of the Yellow Sea,northern China

The colonization features of periphytic protozoa have proved to be a useful tool for indicating water quality status in aquatic ecosystems. In order to reveal the seasonal variations in colonization dynamics of the protozoa, a 1-year baseline survey was carried out in coastal waters of the Yellow Sea, northern China. Using glass slides as artificial substrates, a total of 240 slides were collected at a depth of 1 m in four seasons after colonization periods of 3, 7, 10, 14, 21, and 28 days. A total of 122 ciliate species were identified with 21 dominant species. The colonization dynamics of the protozoa were well fitted to the MacArthur-Wilson and logistic models in all four seasons (P < 0.05). However, the equilibrium species numbers (S_eq), colonization rates (G), and the time to 90% S_eq (T_90%) represented a clear seasonal variability: (1) more or less similar levels in spring and autumn (S_eq = 29/23; G = 0.301/0.296; T_90%=7.650/7.779); (2) with a significant difference in summer and winter (S_eq = 32/121; G = 0.708/0.005; T_90% = 3.252/479.705). Multivariate approaches demonstrated that the exposure time for the species composition and community structure of the protozoa to an equilibrium period were 10–14 days in spring and autumn, but less and more time periods were needed in summer and winter, respectively. Based on the results, we suggest that the colonization dynamics of periphytic protozoa were different within four seasons, and an optimal sampling strategy for monitoring surveys should be modified during different seasons in marine ecosystems.     

Realistic Variation in Species Composition Affects Grassland Production,Resource Use and Invasion Resistance

We investigated the effects of realistic variation in plant species and functional group composition, with species occurring at realistic abundances, on ecosystem processes in exotic-dominated California grassland communities. Progressive species removals from microcosm communities, designed to mimic nested variation in diversity observed in the field, reduced grassland production, resistance to intentional invasions, and resistance to natural colonization by new species. Three lines of evidence point to the particular importance of intensified competition within a single functional group—late-active forbs—in explaining the observed effects of realistic species loss order on community resistance. First, reduced success of naturally colonizing species in more diverse assemblages was dominated by declining colonization by late-active forbs. Second, increasing late-active forb biomass appeared to reduce the biomass of intentionally introduced yellow starthistle (Centaurea solstitialis, a late-season forb) both within and across diversity levels. Finally, starthistle addition reduced biomass of resident late-season forbs but not of any other functional group. Increasing diversity increased light levels and soil moisture availability in spring and summer, providing a proximate mechanism linking our realistic species loss order to decreased community resistance. Starthistle addition reduced light and soil moisture availability but not N across richness levels, mirroring the apparent effects of the additional late-active forb species present in higher diversity treatments. Species losses that entail the early loss of whole or key functional groups could, through mechanisms like those we explore, have greater ecosystem consequences than those suggested by randomized-loss experiments.     

Dynamics of Nutrient Contents (Phosphorus,Nitrogen) in Water,Sediment and Plants After Restoration of Connectivity in Side‐Channels of the River Rhine

During the last century, canalization of the Rhine river led to disconnection of side‐arms, over‐sedimentation of these channels, loss of the fluvial dynamics, and aquatic vegetation change or disappearance. Recent restoration projects aim to reconnect disconnected arms to the main channel. The objective of this study was to assess the nutrient dynamics in restored channels during the vegetation colonization process. In spring, summer, and autumn 2009, the phosphorus and nitrogen contents were measured in water, sediment, and plants, sampled in six channels, two reference sites and four restored ones at different dates. Aquatic vegetation was monitored during the same period. Sites were mesotrophic related to the water nutrient concentrations. However, vegetation communities indicated a eutrophic level, as they were dominated by species like Elodea nuttallii, Myriophyllum spicatum, and Potamogeton perfoliatus. Sites were discriminated by P content and mineral nitrogen in the sediment. We showed an effect of species and season on the plant nutrient content, but there was no relationship between plant nutrient content and nutrients in water and sediment. A negative correlation between mean N plant content and the cover of each species was found. Vegetation characteristics (species richness and cover) and bioavailable phosphorus in the sediment were also correlated. In the restored side‐arms of the river Rhine, phosphorus‐rich sediment seems to be important in the recolonization dynamics, as it was linked to higher species richness, whereas nitrogen played a role in the colonization patterns as a growth limiting factor.     

Photosynthetic parameters from two contrasting woody vegetation types in West Africa

Measurements of leaf gas exchange were made in contrasting wooded ecosystems in West Africa. Measurements were made on 10 species: seven from humid rain forest in Cameroon and three from the semi-arid Sahelian zone in Niger. For each species, two models of photosynthesis were fitted: the first based on a rectangular hyperbolic response to photosynthetic photon flux density (Q), and the second the biochemical model of Farquhar et al. (1980). In both communities, the species studied could be divided into those characteristic of early and late successional stages, but photosynthetic parameters were not closely related to successional stage. The data identified significant relationships between V _cmax and leaf nutrient (N and P) content when expressed on an area basis. Variation in leaf mass per unit area correlated with canopy exposure and dominated the leaf nutrient signal. Statistical analysis suggested weakly that leaf gas exchange was more limited by P than N at the rain forest site.     

Phosphorus,Nitrogen and Chlorophyll-a Are Significant Factors Controlling Ciliate Communities in Summer in the Northern Beibu Gulf,South China Sea

Ciliates (protozoa) are ubiquitous components of plankton community and play important roles in aquatic ecosystems in regards of their abundance, biomass, diversity and energy turnover. Based on the stratified samples collected from the northern Beibu Gulf in August 2011, species composition, abundance, biomass, diversity and spatial pattern of planktonic ciliates were studied. Furthermore the main environmental factors controlling ciliate communities were determined. A total of 101 species belonging to 44 genera and 7 orders (i.e., Oligotrichida, Haptorida, Euplotida, Sessilida, Pleurostomatida, Scuticociliatida and Tintinnida) were identified. The variation of ciliate communities was significant at horizontal level, but that was not at vertical level. Based on cluster analysis, ciliate communities were divided into three main groups. Redundancy analysis (RDA) revealed that Group A, existing in the waters with higher concentration of phosphorus and nitrogen, was dominated by Tintinnidium primitivum. Group B in the waters with lower temperature and chlorophyll-a concentration, was dominated by Leegaardiella ovalis. Group C, existing in the waters with higher temperature and chlorophyll-a concentration, was dominated by large Strombidium spp. and Mesodinium rubrum. Combining multiple analytic methods, our results strongly supported that phosphorus, nitrogen and chlorophyll-a were the most significant factors affecting the ciliate communities in the northern Beibu Gulf in summer. Concentration of phosphorus and nitrogen primarily influenced ciliate biomass, implying a potential impact of eutrophication on ciliate growth. The correlation with chlorophyll-a concentration, on one hand indicate the response of ciliates to the food availability, and on the other hand, the ciliates containing chloroplasts or endosymbionts may contribute greatly to the chlorophyll-a.     

Positive feedback in aquatic ecosystems

Aquatic ecosystems offer striking examples of how positive feedback can be integral to the dynamics of complex communities. In particular, microorganisms (bacteria and protozoa) introduce a multitude of positive feedback pathways by rapidly recycling nutrients at the very base of many aquatic food webs. The relatively large magnitude of fluxes being shunted through this 'microbial loop' allows an accumulation of nutrients in localized areas, promotes a general build-up of biomass, and acts as a 'life-support system' in harsh environments. In contrast to customary notions which portray positive feedback effects as undesirable, a reassessment indicates that this 'bootstrapping' can often be advantageous for many organisms.     

Estimating the growth potential of the soil protozoan community

We have developed a method for determining the potential abundance of free-living protozoa in soil. The method permits enumeration of four major functional groups (flagellates, naked amoebae, testate amoebae, and ciliates) and it overcomes some limitations and problems of the usual 'direct' and 'most probable number' methods. Potential abundance is determined using light microscopy, at specific time intervals, after quantitative re-wetting of air-dried soil with rain water. No exogenous carbon substrates or mineral nutrients are employed, so the protozoan community that develops is a function of the resources and inhibitors present in the original field sample. The method was applied to 100 soil samples (25 plots x 4 seasons) from an upland grassland (Sourhope, Southern Scotland) in the UK. Median abundances for all four functional groups lie close to those derived from the literature on protozoa living in diverse soil types. Flagellates are the most abundant group in soil, followed by the naked amoebae, then the testate amoebae and ciliates. This order is inversely related to typical organism size in each group. Moreover, preliminary evidence indicates that each functional group contains roughly the same number of species. All of these observations would be consistent with soil having fractal structure across the size-scale perceived by protozoa. The method described will be useful for comparing the effects on the soil protozoan community of different soil treatments (e.g. liming and biocides).     

东海原甲藻(Prorocentrum donghaiensis)对原生动物群落结构影响的现场船基实验

2005年在长江口赤潮频发海域调查期间,分别于4月27日、5月4日和5月8日,在zzf1、zc18a和ra5站位利用现场船基培养的方法,研究了添加到赤潮密度10^6cells L^-1的东海原甲藻（Prorocentrum donghaiense）对原生动物群落结构的影响。结果发现,赤潮密度的东海原甲藻抑制了小型无壳纤毛虫的种群数量,而没有抑制中大型砂壳纤毛虫和夜光虫（Noctiluca scintillans）的种群数量,从而使得原生动物群落向中大型种类演替,这种影响的程度与原生动物本身的群落组成和浮游植物的组成密切相关。添加东海原甲藻72h后,在以小型无壳纤毛虫管游虫（Cyrtostrombidium sp．）为优势种的zzf1站位,演替为以大型原生动物夜光虫为优势种的群落;在以中大型原生动物百乐拟铃虫（Tintinnospsis beroidea）和夜光虫为优势种的zc18a站位,仍然是以此为优势种,且大型原生动物夜光虫在群落中的比例上升;在以小型无壳纤毛虫急游虫2（Strombidium sp．2）为优势种的ra5站位,演替为以中大型原生动物百乐拟铃虫和亚速岛网纹虫（Favella azorica）为优势种的群落。zzf1和ra5站位实验组中原生动物的总丰度都呈下降趋势,而zc18a站位变化不明显,这是由于前两个站位的最优势种管游虫（zzf1站位）和急游虫2（ra5站位）的丰度迅速下降,而zc18a站位的优势种百乐拟铃虫和夜光虫的丰度比较稳定造成的。在zzf1和zc18a站位,对照组和实验组中原生动物的总生物量在实验前后都没有大的变化,而在ra5站位却均呈下降的趋势。这可能与浮游植物的组成有关,zzf1和zc18a站位是以无毒的锥状斯氏藻（Scrippsiella trochoidea）和螺旋环沟藻（Gyrodinium spirale）为主,而ra5站位是以有毒的亚历山大藻（Alexandriumsp．）为主。综上可见,可预测当东海大规模赤潮爆发时,会使原生动物群落向中大型种类演替,进而可能影响海洋生态系统的结构和功能。     

Mycorrhizal features and leaf traits covary at the community level during primary succession

The mycorrhizal association between fungi and plants is thought to be an important component of the functional diversity of plant communities, although evidence is weak. We explored community-level changes to mycorrhizal features and leaf traits along a primary successional gradient on a sedimentation coast. We found that community weighted mean values of mycorrhizal features and leaf traits varied systematically along the successional series, representing a transition from communities dominated by more stress-tolerant plant species (less mycorrhizal colonization and lower specific leaf area) to less stress-tolerant plant species (higher mycorrhizal colonization and specific leaf area). Despite the co-variation in leaf traits and mycorrhizal features at the community level, only mycorrhizal features showed an increasing functional diversity with successional age. These results suggest that mycorrhizal fungi should not be forgotten in trait-based plant community ecology.