Testing a ‘genes‐to‐ecosystems’ approach to understanding aquatic–terrestrial linkages

A ‘genes‐to‐ecosystems’ approach has been proposed as a novel avenue for integrating the consequences of intraspecific genetic variation with the underlying genetic architecture of a species to shed light on the relationships among hierarchies of ecological organization (genes → individuals → communities → ecosystems). However, attempts to identify genes with major effect on the structure of communities and/or ecosystem processes have been limited and a comprehensive test of this approach has yet to emerge. Here, we present an interdisciplinary field study that integrated a common garden containing different genotypes of a dominant, riparian tree, Populus trichocarpa, and aquatic mesocosms to determine how intraspecific variation in leaf litter alters both terrestrial and aquatic communities and ecosystem functioning. Moreover, we incorporate data from extensive trait screening and genome‐wide association studies estimating the heritability and genes associated with litter characteristics. We found that tree genotypes varied considerably in the quality and production of leaf litter, which contributed to variation in phytoplankton abundances, as well as nutrient dynamics and light availability in aquatic mesocosms. These ‘after‐life’ effects of litter from different genotypes were comparable to the responses of terrestrial communities associated with the living foliage. We found that multiple litter traits corresponding with aquatic community and ecosystem responses differed in their heritability. Moreover, the underlying genetic architecture of these traits was complex, and many genes contributed only a small proportion to phenotypic variation. Our results provide further evidence that genetic variation is a key component of aquatic–terrestrial linkages, but challenge the ability to predict community or ecosystem responses based on the actions of one or a few genes.     

The role of phytoplankton in the diet of the bladderwort Utricularia australis R.Br. (Lentibulariaceae)

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Evaluation of seasonal dynamics of fungal DNA assemblages in a flow-regulated stream in a restored forest using eDNA metabarcoding

Investigation of seasonal variation in fungal communities is essential for understanding biodiversity and ecosystem functions. However, the conventional sampling method, with substrate removal and high spatial heterogeneity of community composition, makes surveying the seasonality of fungal communities challenging. Recently, water environmental DNA (eDNA) analysis has been explored for its utility in biodiversity surveys. In this study, we assessed whether the seasonality of fungal communities can be detected by monitoring eDNA in a forest stream. We conducted monthly water sampling in a forest stream over 2 years and used DNA metabarcoding to identify fungal eDNA. The stream water contained DNA from functionally diverse aquatic and terrestrial fungi, such as plant decomposers, parasites and mutualists. The variation in the fungal assemblage showed a regular annual periodicity, meaning that the assemblages in a given season were similar, irrespective of the year or sampling. Furthermore, the strength of the annual periodicity varied among functional groups. Our results suggest that forest streams may act as a ‘trap’ for terrestrial fungal DNA derived from different habitats, allowing the analysis of fungal DNA in stream water to provide information about the temporal variation in fungal communities in both the aquatic and the surrounding terrestrial ecosystems.     

Connecting through space and time: catchment-scale distributions of bacteria in soil,stream water and sediment

Terrestrial and aquatic environments are linked through hydrological networks that transport abiotic components from upslope environments into aquatic ecosystems. However, our understanding of how bacteria are transported through these same networks is limited. Here, we applied 16S rRNA gene sequencing to over 500 soil, stream water and stream sediment samples collected within a native forest catchment to determine the extent to which bacterial communities in these habitats are connected. We provide evidence that while the bacterial communities in each habitat were significantly distinct from one another (PERMANOVA pairwise P < 0.001), the bacterial communities in soil and stream samples were weakly connected to each other when stream sediment sample locations were downhill of surface runoff flow paths. This pattern decreased with increasing distance between the soil and sediment samples. The connectivity between soil and stream water samples was less apparent and extremely transient; the greatest similarity between bacterial communities in soil and stream water overall was when comparing stream samples collected 1 week post soil sampling. This study shows how bacterial communities in soil, stream water and stream sediments are connected at small spatial scales and provides rare insights into the temporal dynamics of terrestrial and aquatic bacterial community connectivity.     

Resource limitation,biodiversity, and competitive effects interact to determine the invasibility of rock pool microcosms

The success of species invasions depends on both the characteristics of the invaded habitat and the traits of the invasive species. At local scales biodiversity may act as a barrier to invasion; however, the mechanism by which biodiversity confers invasion resistance to a community has been the subject of considerable debate. The purpose of this study was to test the hypothesis that productivity and diversity affected the ability of a regionally available species to colonize communities from which it is absent. We hypothesized that the invasibility of rock pool invertebrate communities would increase with increasing nutrients and decrease with increasing diversity. We tested this possibility using naturally invaded outdoor aquatic microcosms. We demonstrated that the invasibility of an experimental multi-trophic aquatic community by a competitive native midge species (Ceratopogonidae: Dasyhelea sp.) was determined by an interaction between resource availability, diversity, and the densities of two competitive ostracods species. Nutrient enrichment increased invasion success; however, within nutrient-enriched microcosms, invasion success was highest in the low-diversity treatments. Our results suggest that resource availability may in fact be the principal mechanism determining invasibility at local scales in multi-trophic rock pool communities; however resource availability can be determined by both nutrient input as well as by the diversity of the biotic community.     

物种多样性及环境因子对入侵植物空心莲子草群落稳定性的影响

为探讨外来入侵植物空心莲子草群落稳定性的驱动机制,在中国21°N-37°N范围内设置73个面积为10 mX 10 m的空心莲子草群落样地(陆生39个,水生34个),分别计算其Godron群落稳定性坐标值和4个α-物种多样性指数,并测定各样地的7项环境因子(经度、纬度、海拔、铵态氮、硝态氮、年均温和年均降雨量),采用回归...     

荒漠草原盐沼湿地苦豆子土壤细菌群落构建机制及其影响因素

【背景】荒漠草原盐沼湿地是陆地生态系统的重要组成部分,土壤水分和盐分变化是影响该生态系统土壤细菌群落构建的重要因素。【目的】土壤细菌群落构建是由确定性和随机性主导的连续生态过程,阐明荒漠草原盐沼湿地土壤细菌群落的构建机制对于加深微生物作为关键生态系统因子重要性的理解具有积极意义。【方法】以宁夏中部典型荒漠草原盐沼苦水湖湿地为研究对象,对近湖边（near the lake,NL）和远离湖边（far from the lake,FL）苦豆子群落土壤理化特性进行测定并结合土壤细菌高通量测序分析。【结果】NL和FL样地具有明显的水盐梯度变化,NL样地土壤pH、含水量和电导率均显著高于FL样地;变形菌门、放线菌门、厚壁菌门、拟杆菌门和黏菌门是研究区域土壤细菌群落的优势菌门,变形菌门相对丰度随水盐梯度上升而升高,放线菌门和厚壁菌门相对丰度则随之下降,门下成员大多与水盐变化具有明显的相关性;此外,FL样地土壤细菌网络则具有稳定的网络关系;随着NL样地向FL样地的延伸,土壤细菌群落由随机过程主导,并且受pH、电导率和环境变量的影响。【结论】荒漠草原盐沼湿地水分和盐分的变化改变了土壤细菌群落结构;土壤细菌群落通过生态位占据等策略提高逆境下的生存能力;细菌群落构建是随机过程和确定性过程组成的连续统一体,同样受环境变化的影响。本结果揭示了荒漠草原盐沼湿地细菌群落结构和相互关系对环境变化的响应特征,同时阐明了该区土壤细菌群落的构建机制及影响因素,也为相关科学研究提供了一定理论参考。     

AM fungal communities inhabiting the roots of submerged aquatic plant <Emphasis Type="Italic">Lobelia dortmanna</Emphasis> are diverse and include a high proportion of novel taxa

While the arbuscular mycorrhizal (AM) symbiosis is known to be widespread in terrestrial ecosystems, there is growing evidence that aquatic plants also form the symbiosis. It has been suggested that symbiosis with AM fungi may represent an important adaptation for isoëtid plants growing on nutrient-poor sediments in oligotrophic lakes. In this study, we address AM fungal root colonization intensity, richness and community composition (based on small subunit (SSU) ribosomal RNA (rRNA) gene sequencing) in five populations of the isoëtid plant species Lobelia dortmanna inhabiting oligotrophic lakes in Southern Sweden. We found that the roots of L. dortmanna hosted rich AM fungal communities and about 15 % of the detected molecular taxa were previously unrecorded. AM fungal root colonization intensity and taxon richness varied along an environmental gradient, being higher in oligotrophic and lower in mesotrophic lakes. The overall phylogenetic structure of this aquatic fungal community differed from that described in terrestrial systems: The roots of L. dortmanna hosted more Archaeosporaceae and fewer Glomeraceae taxa than would be expected based on global data from terrestrial AM fungal communities.     

Intermittent Pool Beds Are Permanent Cyclic Habitats with Distinct Wet,Moist and Dry Phases

Recognition that intermittent pools are a single habitat phase of an intermittent pool bed that cycles between aquatic and terrestrial habitat greatly enhances their usefulness for addressing general questions in ecology. The aquatic phase has served as a model system in many ecological studies, because it has distinct habitat boundaries in space and time and is an excellent experimental system, but the aquatic to terrestrial transition and terrestrial phase remain largely unstudied. We conducted a field experiment within six replicate natural intermittent pool beds to explore macroinvertebrate community dynamics during the transition from aquatic to terrestrial habitat and during the terrestrial phase. We monitored and compared macroinvertebrate communities within leaf packs that i) remained wet, ii) underwent drying (i.e., started wet and then dried), and iii) remained dry. Our results show that i) a diverse macroinvertebrate community inhabits all phases of intermittent pool beds, ii) pool drying involves colonization by an assemblage of macroinvertebrates not recorded in permanently terrestrial leaf packs, iii) the community within dried leaf packs remains distinct from that of permanently terrestrial leaf packs for an extended period following drying (possibly until subsequent refilling), and iv) there are likely to be strong spatial and temporal resource linkages between the aquatic and terrestrial communities. The unique environmental characteristics of intermittent pool beds, which repeatedly cycle from aquatic to terrestrial habitat, should continue to make them valuable study systems.     

Ectomycorrhizal fungal community structure across a bog-forest ecotone in southeastern Alaska

We examined the ectomycorrhizal (ECM) fungal community across a bog-forest ecotone in southeastern Alaska. The bog and edge were both characterized by poorly drained Histosols and a continuous layer of Sphagnum species, ericaceous shrubs, Carex species, and shore pine [Pinus contorta Dougl. ex Loud. var. contorta]. The forest had better-drained Inceptisols and Spodosols, a tree community comprised of western hemlock [Tsuga heterophylla (Raf.) Sarg.], yellow cedar (Thuja plicata Donn ex D. Don.), Sitka spruce [Picea sitchensis (Bong.) Carr.] and shore pine, and an understorey of ericaceous shrubs and herbs. ECM root tip density (tips cm^–3 soil) was significantly greater in the forest than the edge or bog and ECM colonization was significantly different in all three plant communities. The below ground ECM fungal taxa were analyzed using molecular techniques (PCR-RFLP and DNA sequencing). Three ECM fungal taxa, Suillus tomentosus (Kauffman) Singer, Cenococcum geophilum Fr.:Fr, and a Russula species, differed in relative frequency, yet were among the four most frequent in all three plant communities. Although differences in ECM fungal richness were observed across plant communities, unequal sampling of ECM roots due to root density and colonization differences confounded richness comparisons. Using resampling procedures for creating taxon-accumulation curves as a function of sampled ECM roots revealed similarities in cumulative ECM fungal taxa richness across the ecotone.     

A Hypothetical Application of the Pollution-Induced Community Tolerance Concept in Megafaunal Communities Found at Contaminated Sites

The purpose of our paper is to suggest a novel, hypothetical and yet untested use of the pollution-induced community tolerance concept (PICT). Historically, PICT has been applied to determine whether toxicants are deleterious in microfaunal aquatic and terrestrial communities. We hypothesize that it may be possible to apply PICT to megafaunal organisms (e.g., vertebrates). In doing so, researchers could (1) identify which toxicant, in a complex mixture of toxicants, is harmful since only those contaminants that exert selection pressure are biologically relevant and will result in changes in community structure and (2) determine the transfer of toxicants across trophic levels found within that community. We suggest that community tolerance could be measured in megafaunal communities by measuring biomarkers of exposure and effect in either a number of individuals that make up different populations of animals comprising a community, or in the community as a whole. In this article we discuss the theoretical suitability of our megafaunal PICT approach to the assessment of contaminated sites and some of the potential pitfalls associated with its use. Our intention is that this paper will generate debate and commentary surrounding PIGT and its potential uses in the future. Whether this potential approach is feasible remains to be determined.     

Testate amoebae community pattern in different types of boundary structures at the water-land contact zone

The patterns of changes in the species richness, abundance, species composition, and species structure of the testate amoebae community along six different types of water-land boundaries in the Medveditsa River (Don river Basin) were studied, namely, a new boundary, terrigenous and reogeneous edges, reogeneous and terrigenous hemiecotones, and the full ecotone. The testate amoebae communities are divided into terrestrial and aquatic variants for all types of boundaries. Hydrophilic species of the genera Arcella, Diffugia, Cyphoderia, and Pseudodifflugia dominate in the aquatic types of communities while pedobiont and eurybiont groups from the genera Centropyxis, Euglypha, Plagiopyxis, and Trinema are characteristic of the terrestrial communities. A decrease in the abundance and species richness of testate amoebae in the boundary zones was detected.     

氧化石墨烯对黑麦草种子内生真菌群落结构和多样性的影响

为了探究氧化石墨烯(GO)对黑麦草种子内生真菌群落结构和多样性的影响,将黑麦草种子在0.4%、0.8%和1.2%水平的GO溶液中胁迫4 d,采用高通量测序技术,分析GO胁迫下黑麦草种子内生真菌群落组成和多样性的变化。结果显示,4个样本所有样品共分离获得303种真菌,归属于10门39纲84目160科240属。在门分类水平上,子囊菌门(Ascomycota)和担子菌门(Basidiomycota)是主要的内生真菌类群;在属分类水平上,各处理的共有优势菌属为链格孢属(Alternaria)。不同GO处理黑麦草种子内生真菌群落结构存在差异,随着GO浓度的增加,子囊菌门的丰度出现下降,0.8%和1.2%GO处理较对照分别显著降低了19%和20%(P<0.05);所有GO处理的担子菌门丰度均显著高于对照(P<0.05);1.2%处理链格孢属的丰度较对照显著降低了37.36%。与对照相比,1.2%GO 处理内生真菌的丰富度和多样性显著增加,ACE、Chao1和Shannon指数分别增加了123.5%、127.4%和117.5%(P<0.05)。主坐标分析(PCoA)分析表明,1.2%GO处理内生真菌群落结构与其他处理有较大差异;线性判别分析(LEfSe)分析发现, 各处理差异指示种明显不同。可见,GO改变了黑麦草种子内生真菌群落的组成和多样性,尤其是高浓度处理(1.2%)。研究可为碳纳米材料暴露对共生物种的潜在影响研究提供参考。     

澜沧江两条支流捕食线虫真菌水陆分布差异及关联性

为探究微生物在流域中的水、陆分布差异和相互关系,对澜沧江两条支流捕食线虫真菌多样性水陆分布进行了调查研究。在枯水期,以澜沧江一级支流沘江和黑惠江为研究区域,系统布设12个采样点(水流交汇点),每个采样点采集水、陆对称样品各5份,共采集土样120份。结合传统分离纯化、形态学及分子生物学方法筛选和鉴定菌株,按照《Nematode-Trapping Fungi》进行分类,共获得2属13种88株捕食线虫真菌;其中,陆地样品中共分离到2属11种45株,水体底泥中分离出1属10种43株,检出率分别为41.67%和53.33%。结果表明,澜沧江两条支流捕食线虫真菌在物种、属、群落结构3个层面上均存在水陆差异,也相互联系;陆地土壤可能是流域内捕食线虫真菌多样性的源,水流是其重要的传播因子。在流域生态系统内,水陆间的扩散限制和水流的连通性都是维持微生物物种多样性的重要机制。     

Towards robust and repeatable sampling methods in eDNA‐based studies

DNA‐based techniques are increasingly used for measuring the biodiversity (species presence, identity, abundance and community composition) of terrestrial and aquatic ecosystems. While there are numerous reviews of molecular methods and bioinformatic steps, there has been little consideration of the methods used to collect samples upon which these later steps are based. This represents a critical knowledge gap, as methodologically sound field sampling is the foundation for subsequent analyses. We reviewed field sampling methods used for metabarcoding studies of both terrestrial and freshwater ecosystem biodiversity over a nearly three‐year period (n = 75). We found that 95% (n = 71) of these studies used subjective sampling methods and inappropriate field methods and/or failed to provide critical methodological information. It would be possible for researchers to replicate only 5% of the metabarcoding studies in our sample, a poorer level of reproducibility than for ecological studies in general. Our findings suggest greater attention to field sampling methods, and reporting is necessary in eDNA‐based studies of biodiversity to ensure robust outcomes and future reproducibility. Methods must be fully and accurately reported, and protocols developed that minimize subjectivity. Standardization of sampling protocols would be one way to help to improve reproducibility and have additional benefits in allowing compilation and comparison of data from across studies.     

Microbial Community Changes Elicited by Exposure to Cyanobacterial Allelochemicals

An increasing body of evidence points out that allelopathy may be an important process shaping microbial communities in aquatic ecosystems. Cyanobacteria have well-documented allelopathic properties, mainly derived from the evaluation of the activity of allelopathic extracts or pure compounds towards monocultures of selected target microorganisms. Consequently, little is known regarding the community dynamics of microorganisms associated with allelopathic interactions. In this laboratory-based study, a Microcystis spp.-dominated microbial community from a freshwater lake was exposed, for 15 days, to exudates from the cyanobacterium Oscillatoria sp. strain LEGE 05292 in laboratory conditions. This cyanobacterium is known to produce the allelochemicals portoamides, which were among the exuded compounds. The community composition was followed (by means of polymerase chain reaction followed by denaturing gradient gel electrophoresis and microscopic analyses) and compared to that of a non-exposed situation. Following exposure, clear differences in the community structure were observed, in particular for cyanobacteria and unicellular eukaryotic taxa. Interestingly, distinct Microcystis genotypes present in the community were differentially impacted by the exposure, highlighting the fine-scale dynamics elicited by the exudates. These results support a role for cyanobacterial allelochemicals in the structuring of aquatic microbial communities.     

Revisiting the ‘bank of microscopic forms’ in macroalgal‐dominated ecosystems

Theoretical ecological models, such as succession and facilitation, were defined in terrestrial habitats, and subsequently applied to marine and freshwater habitats in intertidal and then subtidal realms. One such model is the soil seed bank, defined as all viable seeds (or fruits) found near the soil surface that facilitate community restoration/recovery. “Banks of microscopic forms” have been hypothesized in aquatic habitats and recent work from aquaculture has highlighted dormancy in algal life cycle stages. To reinvigorate the discussions about these algal banks, we discuss differences in life cycles, dispersal, and summarize research on banks of macroalgal stages in aquatic ecosystems that may be easier to explore with modern advances in molecular technology. With focus on seminal work in global kelp forest ecosystems, we present a pilot study in northern California as proof of concept that Nereocystis luetkeana and Alaria marginata stages can be detected within kelp forests in the biofilm of rocks and bedrock using targeted primers long after zoospore release. Considering the increased interest in algae as an economic resource, [blue] carbon sink, and as ecosystem engineers, the potential for “banking” macroalgal forms could be a mechanism of resilience and recovery in aquatic populations that have complex life cycles and environmental cues for reproduction. Molecular barcoding is becoming an important tool for identifying banks of macroalgal forms in marine communities. Understanding banks of macroalgal stages, especially in deforested habitats with intense disturbance and grazer pressure, will allow researchers and marine resource managers to facilitate this natural process in recovery of the aquatic system.     

Terrestrial contributions to Afrotropical aquatic food webs: The Congo River case

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Prolonged exposure to manure from livestock‐administered antibiotics decreases ecosystem carbon‐use efficiency and alters nitrogen cycling

Microbial communities drive soil ecosystem function but are also susceptible to environmental disturbances. We investigated whether exposure to manure sourced from cattle either administered or not administered antibiotics affected microbially mediated terrestrial ecosystem function. We quantified changes in microbial community composition via amplicon sequencing, and terrestrial elemental cycling via a stable isotope pulse‐chase. Exposure to manure from antibiotic‐treated cattle caused: (i) changes in microbial community structure; and (ii) alterations in elemental cycling throughout the terrestrial system. This exposure caused changes in fungal : bacterial ratios, as well as changes in bacterial community structure. Additionally, exposure to manure from cattle treated with pirlimycin resulted in an approximate two‐fold increase in ecosystem respiration of recently fixed‐carbon, and a greater proportion of recently added nitrogen in plant and soil pools compared to the control manure. Manure from antibiotic‐treated cattle therefore affects terrestrial ecosystem function via the soil microbiome, causing decreased ecosystem carbon use efficiency, and altered nitrogen cycling.     

Plant communities as a tool in temporary ponds conservation in SW Portugal

Temporary ponds are seasonal wetlands annually subjected to extreme and unstable ecological conditions, neither truly aquatic nor truly terrestrial. This habitat and its flora have been poorly studied and documented because of the ephemeral character of the flora, the changeable annual weather that has a great effect on the small, herbaceous taxa and the declining abundance of temporary ponds. The objectives of this study are: (a) to define plant community diversity in terms of floristic composition of ephemeral wetlands in SW Portugal, (b) to identify temporary pond types according to their vegetation composition and (c) to identify those ponds that configure the European community priority habitat (3170* – Mediterranean temporary ponds). Vegetation sampling was conducted in 29 ponds, identifying 168 species grouped among 15 plant communities. Soil texture, pH, organic C and N content were measured, but only N and percent of clay appear to be related with the distribution of each community type. The results showed that ephemeral wetlands could be classified into four type: vernal pools, marshlands, deep ponds and disturbed wetlands. Vernal pools correspond to the Mediterranean temporary ponds (3170*), protected as priority habitat under the EU Habitats Directive. Submersed Isoetes species (Isoetes setaceum and Isoetes velatum) represents, together with Eryngium corniculatum, the indicator species for vernal pools. We identify also indicator plant communities of this priority habitat, namely I. setaceum and E. corniculatum–Baldellia ranunculoides plant communities. In this region, the conservation of temporary ponds has so far been compatible with traditional agricultural activities, but today these ponds are endangered by the intensification of agriculture and the loss of traditional land use practices and by the development of tourism. Guest editors: B. Oertli, R. Cereghino, A. Hull & R. Miracle Pond Conservation: From Science to Practice. 3rd Conference of the European Pond Conservation Network, Valencia, Spain, 14–16 May 2008