Measuring habitat complexity and spatial heterogeneity in ecology

Habitat complexity has been considered a key driver of biodiversity and other ecological phenomena for nearly a century. However, there is still no consensus over the definition of complexity or how to measure it. Up-to-date and clear guidance on measuring complexity is urgently needed, particularly given the rise of remote sensing and advent of technologies that allow environments to be scanned at unprecedented spatial extents and resolutions. Here we review how complexity is measured in ecology. We provide a framework for metrics of habitat complexity, and for the related concept of spatial heterogeneity. We focus on the two most commonly used complexity metrics in ecology: fractal dimension and rugosity. We discuss the pros and cons of these metrics using practical examples from our own empirical data and from simulations. Fractal dimension is particularly widely used, and we provide a critical examination of it drawing on research from other scientific fields. We also discuss informational metrics of complexity and their potential benefits. We chart a path forward for research on measuring habitat complexity by presenting, as a guide, sets of essential and desirable criteria that a metric of complexity should possess. Lastly, we discuss the applied significance of our review.

Denitrification of Permeable Sand Sediment in a Headwater River Is Mainly Influenced by Water Chemistry, Rather Than Sediment Particle Size and Heterogeneity

Sediment particle size and heterogeneity play an important role in sediment denitrification through direct and indirect effects on, for example, the material exchange rate, environmental gradients, microbial biomass, and grazing pressure. However, these effects have mostly been observed in impermeable sediments. On the other hand, the material exchange of permeable sediments is dominated by advection instead of diffusion, with the exchange or transport rates exceeding those of diffusion by two orders of magnitude relative to impermeable sediments. The impact of permeable sediment particle size and heterogeneity on denitrification remains poorly understood, especially at the millimeter scale. Here, we conducted an in situ control experiment in which we sorted sand sediment into four homogeneous-particle-sizes treatments and four heterogeneous treatments. Each treatment was deployed, in replicate, within the riffle in three different river reaches with contrasting physicochemical characteristics. After incubating for three months, sediment denitrifier communities (nirS, nirK, nosZ), denitrification gene abundances (nirS, nirK, nosZ), and denitrification rates in all treatments were measured. We found that most of the denitrifying microbes in permeable sediments were unclassified denitrifying microbes, and particle size and heterogeneity were not significantly correlated with the functional gene abundances or denitrification rates. Water chemistry was the key controlling factor for the denitrification of permeable sediments. Water NO3--N directly regulated the denitrification rate of permeable sediments, instead of indirectly regulating the denitrification rate of sediments by affecting the chemical characteristics of the sediments. Our study fills a knowledge gap of denitrification in permeable sediment in a headwater river and highlights that particle size and heterogeneity are less important for permeable sediment denitrification.

Nitrogen removal enhanced by benthic bioturbation coupled with biofilm formation: A new strategy to alleviate freshwater eutrophication

Excessive nitrogen input into the water caused eutrophication thereby reducing biodiversity and degrades freshwater function. Nitrogen pollution in sediments is one key reason that makes eutrophication difficult to control. The physicochemical technologies such as dredging and coverage for sediment pollution easily destroyed and homogenized aquatic habitats. To alleviate freshwater eutrophication in ecological way, this work combined the functions of bioturbation and biofilm to test their effect on the removal of nitrogen from sediment and water. The total nitrogen removal by employing the coupled function (bioturbation + biofilm, SCB) was greater than that of the single function (bioturbation or biofilm). The mean efficiency of total nitrogen removal in SCB treatment was 3.19 times that of the control without chironomids nor biofilm medium. Chironomid bioturbation promoted nitrogen release from sediments to the overlying water. Biofilm enhanced the conversion and removal of nitrogen stirred up by chironomids, resulting the lowest concentration of total nitrogen in overlying water of SCB treatment. The enhancement of nitrogen removal may be due to the coupled function increased the abundance of denitrifying and anammox functional bacteria in sediment and biofilm. Therefore, the method of combining benthic animals with biofilm medium is not only a viable solution for reducing sedimentary nitrogen loading in freshwater ecosystems, but also a solution to mitigate eutrophication in the overlying water. The restoration and management for aquatic ecosystems should consider protecting habitat for benthic organisms while maintaining heterogeneity for biofilm.

Microbiome of permeable sandy substrate in headwater river is shaped by water chemistry rather than grain size and heterogeneity

The reservoir of microbial communities within the soil and the sediment performs many ecological functions and offers many ecosystem services. It has been suggested that its diversity and community structure could be explained by different grain size and heterogeneity. However, most of these conclusions come from studies conducted in terrestrial soil, impermeable marine and freshwater sediment (substrate). It remains to be seen whether these conclusions hold true in permeable substrate, especially in headwater river ecosystems. To address this, a field experiment was aimed to evaluate the link between grain median size and distribution heterogeneity and microbial diversity and community structure. Permeable substrate with gradient grain sizes and heterogeneities was inoculated in a headwater river in central China, while the diversity and community composition of the total microbial community and three denitrifier communities were investigated by high throughput sequencing three months later. The total microbial community was sequenced by 16S rRNA, a marker for taxonomic diversity. Three denitrifier communities were sequenced using three functional gene markers: nirK, nirS, and nosZ. The result showed that both the diversity and community structure of the total microbial community and three denitrifier communities were determined by water chemistry rather than grain size and size distribution heterogeneity, although grain size and heterogeneity positively influenced the nutrient concentrations of the substrate. Compared to the total microbial community, denitrification functional groups had more unique species proportions, indicating that functional genes were more sensitive to environmental change than the 16S rRNA gene. Our study fills a gap in understanding microbial communities in permeable sediment in a headwater river and highlights the less importance of grain size and heterogeneity on mm-scale in shaping the diversity and structure of microbiome.

The Lichens' Microbiota, Still a Mystery?

Lichens represent self-supporting symbioses, which occur in a wide range of terrestrial habitats and which contribute significantly to mineral cycling and energy flow at a global scale. Lichens usually grow much slower than higher plants. Nevertheless, lichens can contribute substantially to biomass production. This review focuses on the lichen symbiosis in general and especially on the model species Lobaria pulmonaria L. Hoffm., which is a large foliose lichen that occurs worldwide on tree trunks in undisturbed forests with long ecological continuity. In comparison to many other lichens, L. pulmonaria is less tolerant to desiccation and highly sensitive to air pollution. The name-giving mycobiont (belonging to the Ascomycota), provides a protective layer covering a layer of the green-algal photobiont (Dictyochloropsis reticulata) and interspersed cyanobacterial cell clusters (Nostoc spec.). Recently performed metaproteome analyses confirm the partition of functions in lichen partnerships. The ample functional diversity of the mycobiont contrasts the predominant function of the photobiont in production (and secretion) of energy-rich carbohydrates, and the cyanobiont's contribution by nitrogen fixation. In addition, high throughput and state-of-the-art metagenomics and community fingerprinting, metatranscriptomics, and MS-based metaproteomics identify the bacterial community present on L. pulmonaria as a surprisingly abundant and structurally integrated element of the lichen symbiosis. Comparative metaproteome analyses of lichens from different sampling sites suggest the presence of a relatively stable core microbiome and a sampling site-specific portion of the microbiome. Moreover, these studies indicate how the microbiota may contribute to the symbiotic system, to improve its health, growth and fitness.

Hydromorphologic Sorting of In-Stream Nitrogen Uptake Across Spatial Scales

Nitrogen (N) uptake is a key process in stream ecosystems that is mediated mainly by benthic microorganisms (biofilms on different substrata) and has implications for the biogeochemical fluxes at catchment scale and beyond. Here, we focused on the drivers of assimilatory N uptake, especially the effects of hydromorphology and other environmental constraints, across three spatial scales: micro, meso and reach. In two seasons (summer and spring), we performed whole-reach 15N-labelled ammonium injection experiments in two montane, gravel-bed stream reaches with riffle–pool sequences. N uptake was highest in epilithic biofilms, thallophytes and roots (min–max range 0.2–545.2 mg N m−2 day−1) and lowest in leaves, wood and fine benthic organic matter (0.05–209.2 mg N m−2 day−1). At the microscale, N uptake of all primary uptake compartments except wood was higher in riffles than in pools. At the mesoscale, hydromorphology determined the distribution of primary uptake compartments, with fast-flowing riffles being dominated by biologically more active compartments and pools being dominated by biologically less active compartments. Despite a lower biomass of primary uptake compartments, mesoscale N uptake was 1.7–3.0 times higher in riffles than in pools. At reach scale, N uptake ranged from 79.6 to 334.1 mg N m−2 day−1. Highest reach-scale N uptake was caused by a bloom of thallopyhtes, mainly filamentous autotrophs, during stable low discharge and high light conditions. Our results reveal the important role of hydromorphologic sorting of primary uptake compartments at mesoscale as a controlling factor for reach-scale N uptake in streams.

Streambed Organic Matter Controls on Carbon Dioxide and Methane Emissions from Streams

Greenhouse gas (GHG) emissions of carbon dioxide (CO₂) and methane (CH₄) from streambeds are currently understudied. There is a paucity of research exploring organic matter (OM) controls on GHG production by microbial metabolic activity in streambeds, which is a major knowledge gap given the increased inputs of allochthonous carbon to streams, especially in agricultural catchments. This study aims to contribute to closing this knowledge gap by quantifying how contrasting OM contents in different sediments affect streambed GHG production and associated microbial metabolic activity. We demonstrate, by means of an incubation experiment, that streambed sediments have the potential to produce substantial amounts of GHG, controlled by sediment OM quantity and quality. We observed streambed CO₂ production rates that can account for 35% of total stream evasion estimated in previous studies, ranging between 1.4 and 86% under optimal conditions. Methane production varied stronger than CO₂ between different geologic backgrounds, suggesting OM quality controls between streambed sediments. Moreover, our results indicate that streambed sediments may produce much more CO₂ than quantified to date, depending on the quantity and quality of the organic matter, which has direct implications for global estimates of C fluxes in stream ecosystems.

Ecological assessment of river networks: From reach to catchment scale

Freshwater ecosystems are increasingly under threat as they are confronted with multiple anthropogenic impairments. This calls for comprehensive management strategies to counteract, or even prevent, long-term impacts on habitats and their biodiversity, as well as on their ecological functions and services. The basis for the efficient management and effective conservation of any ecosystem is sufficient knowledge on the state of the system and its response to external influence factors. In freshwater ecosystems, state information is currently drawn from ecological assessments at the reach or site scale. While these assessments are essential, they are not sufficient to assess the expected outcome of different river restoration strategies, because they do not account for important characteristics of the whole river network, such as habitat connectivity or headwater reachability. This is of particular importance for the spatial prioritization of restoration measures. River restoration could be supported best by integrative catchment-scale ecological assessments that are sensitive to the spatial arrangement of river reaches and barriers. Assessments at this scale are of increasing interest to environmental managers and conservation practitioners to prioritize restoration measures or to locate areas worth protecting. We present an approach based on decision support methods that integrates abiotic and biotic ecological assessments at the reach-scale and aggregates them spatially to describe the ecological state of entire catchments. This aggregation is based on spatial criteria that represent important ecological catchment properties, such as fish migration potential, resilience, fragmentation and habitat diversity in a spatially explicit way. We identify the most promising assessment criteria from different alternatives based on theoretical considerations and a comparison with biological indicators. Potential applications are discussed, particularly for supporting the strategic, long-term planning and spatial prioritization of restoration measures.

Distinct community structure and microbial functions of biofilms colonizing microplastics

Microplastics are frequently detected in freshwater environments, serving as a new factitious substrate for colonization of biofilm-forming microorganisms. Distinct microbial assemblages between microplastics and surrounding waters have been well documented; however, there is insufficient knowledge regarding biofilm colonization of plastic and non-plastic substrates, despite the fact that microbial communities generally aggregate on natural solid surfaces. In this study, the effects of substrate type on microbial communities were evaluated by incubation of biofilms on microplastic substrates (polyethylene and polypropylene) and natural substrates (cobblestone and wood) for 21 days under controlled conditions. Results from high-throughput sequencing of 16S rRNA revealed that the alpha diversity (richness, evenness, and diversity) was lower in the microplastic-associated communities than in those on the natural substrates, indicating substrate-type-coupled species sorting. Distinct community structure and biofilm composition were observed between these two substrate types. Significantly higher abundances of Pirellulaceae, Phycisphaerales, Cyclobacteriaceae, and Roseococcus were observed on the microplastic substrates compared with the natural substrates. Simultaneously, the functional profiles (KEGG) predicted by Tax4Fun showed that the pathways of amino acid metabolism and metabolism of cofactors and vitamins were increased in biofilms on the microplastic substrates. The findings illustrate that microplastic acts as a distinct microbial habitat (compared with natural substrates) that could not only change the community structure but also affect microbial functions, potentially impacting the ecological functions of microbial communities in aquatic ecosystems.

Responses of stream microbes to multiple anthropogenic stressors in a mesocosm study

Stream ecosystems are affected by multiple anthropogenic stressors worldwide. Even though effects of many single stressors are comparatively well studied, the effects of multiple stressors are difficult to predict. In particular bacteria and protists, which are responsible for the majority of ecosystem respiration and element flows, are infrequently studied with respect to multiple stressors responses. We conducted a stream mesocosm experiment to characterize the responses of single and multiple stressors on microbiota. Two functionally important stream habitats, leaf litter and benthic phototrophic rock biofilms, were exposed to three stressors in a full factorial design: fine sediment deposition, increased chloride concentration (salinization) and reduced flow velocity. We analyzed the microbial composition in the two habitat types of the mesocosms using an amplicon sequencing approach. Community analysis on different taxonomic levels as well as principle component analyses (PCoAs) based on realtive abundances of operational taxonomic units (OTUs) showed treatment specific shifts in the eukaryotic biofilm community. Analysis of variance (ANOVA) revealed that Bacillariophyta responded positively salinity and sediment increase, while the relative read abundance of chlorophyte taxa decreased. The combined effects of multiple stressors were mainly antagonistic. Therefore, the community composition in multiply stressed environments resembled the composition of the unstressed control community in terms of OTU occurrence and relative abundances.

Shading and sediment structure effects on stream metabolism resistance and resilience to infrequent droughts

Perennial, temperate, low-order streams are predicted to become intermittent as a result of irregular droughts caused by global warming and increased water demand. We hypothesize that stream metabolism changes caused by irregular droughts are linked to the shading and bed sediment structure of temperate streams. We set up 16 outdoor experimental streams with low or high shade conditions and streambeds either with alternating sorted patches of gravel and sand or homogeneous gravel-sand mix sediment structures. We assessed community respiration (CR), net ecosystem production (NEP) and periphyton biomass and structure (diatoms, green algae, cyanobacteria) in the course of 6weeks colonization, 6weeks desiccation, and 2.5weeks after rewetting. The heterotroph to autotroph (H:A) and fungi to bacteria (F:B) ratios in the microbial biofilm community were assessed at the end of the colonization and rewetting phases. Streams with different bed sediment structure were functionally similar; their metabolism under desiccation was controlled solely by light availability. During flow recession, all streams showed net heterotrophy. As desiccation progressed, NEP and CR decreased to zero. Desiccation altered the periphyton composition from predominantly diatoms to green algae and cyanobacteria, particularly in streams with low shade and mixed sediments. Rapid post-drought resilience of NEP was accompanied by high cyanobacteria and green algae growth in low shade, but poor total periphyton growth in high shade streams. Variable periphyton recovery was followed by increased H:A in relation to shading, and decreased F:B in relation to sediments structure. These shifts resulted in poor CR recovery compared to the colonization phase, suggesting a link between CR resilience and microbial composition changes. The links between drought effects, post-drought recovery, shading level, and streambed structure reveal the importance of low-order stream management under a changing climate and land use to mitigate the future impact of unpredictable infrequent droughts on stream metabolism in temperate ecosystems.

Trophic positioning of meiofauna revealed by stable isotopes and food web analyses

Despite important advances in the ecology of river food webs, the strength and nature of the connection between the meio- and macrofaunal components of the web are still debated. Some unresolved issues are the effects of the inclusion of meiofaunal links and their temporal variations on the overall river food web properties, and the significance of autochthonous and allochthonous material for these components. In the present study, we conducted analyses of gut content of macro- and meiofauna and stable isotope analyses of meiofauna to examine seasonal food webs of a chalk stream. The results of the gut content analyses, confirmed by the δ¹³ C signatures, revealed a seasonal shift from a dependence on autochthonous (biofilm) to allochthonous food sources. Here, we demonstrate that aggregating basal or meiofaunal species into single categories affects key web properties such as web size, links, linkage density, and predator-prey ratios. More importantly, seasonal variation in attributes characterized the entire web and these changes persist regardless of taxonomic resolution. Furthermore, our analyses evidenced discrete variations in δ¹⁵ N across the meiofauna community with a trophic structure that confirms gut content analyses, placing the meiofauna high in the food web. We, therefore, conclude that small-body-sized taxa can occur high in dynamic river food webs, questioning assumptions that trophic position increases with body size and that webs are static.

BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities

Recent advances focusing on the metabolic interactions within and between cellular populations have emphasized the importance of microbial communities for human health. Constraint-based modeling, with flux balance analysis in particular, has been established as a key approach for studying microbial metabolism, whereas individual-based modeling has been commonly used to study complex dynamics between interacting organisms. In this study, we combine both techniques into the R package BacArena (https://cran.r-project.org/package=BacArena) to generate novel biological insights into Pseudomonas aeruginosa biofilm formation as well as a seven species model community of the human gut. For our P. aeruginosa model, we found that cross-feeding of fermentation products cause a spatial differentiation of emerging metabolic phenotypes in the biofilm over time. In the human gut model community, we found that spatial gradients of mucus glycans are important for niche formations which shape the overall community structure. Additionally, we could provide novel hypothesis concerning the metabolic interactions between the microbes. These results demonstrate the importance of spatial and temporal multi-scale modeling approaches such as BacArena.

In nature, organisms are typically found in near proximity to each other, forming symbiotic relationships. Particularly bacteria are often part of highly organized communities such as biofilms. In this study, we integrate the detailed knowledge about the metabolic capabilities of individual organisms into an individual-based modeling approach for simulating the dynamics of local interactions. We provide a fast and flexible framework, in which established computational models for individual organisms can be simulated in communities. Nutrients can diffuse in an area where cells move, divide, and die. The resulting spatial as well as temporal dynamics and metabolic interactions can be analyzed as well as visualized and subsequently compared to experimental findings. We demonstrate how our approach can be used to gain novel insights on dynamics in single species biofilm formation and multi-species intestinal microbial communities.

Habitat Complexity in Aquatic Microcosms Affects Processes Driven by Detritivores

Habitat complexity can influence predation rates (e.g. by providing refuge) but other ecosystem processes and species interactions might also be modulated by the properties of habitat structure. Here, we focussed on how complexity of artificial habitat (plastic plants), in microcosms, influenced short-term processes driven by three aquatic detritivores. The effects of habitat complexity on leaf decomposition, production of fine organic matter and pH levels were explored by measuring complexity in three ways: 1. as the presence vs. absence of habitat structure; 2. as the amount of structure (3 or 4.5 g of plastic plants); and 3. as the spatial configuration of structures (measured as fractal dimension). The experiment also addressed potential interactions among the consumers by running all possible species combinations. In the experimental microcosms, habitat complexity influenced how species performed, especially when comparing structure present vs. structure absent. Treatments with structure showed higher fine particulate matter production and lower pH compared to treatments without structures and this was probably due to higher digestion and respiration when structures were present. When we explored the effects of the different complexity levels, we found that the amount of structure added explained more than the fractal dimension of the structures. We give a detailed overview of the experimental design, statistical models and R codes, because our statistical analysis can be applied to other study systems (and disciplines such as restoration ecology). We further make suggestions of how to optimise statistical power when artificially assembling, and analysing, 'habitat complexity' by not confounding complexity with the amount of structure added. In summary, this study highlights the importance of habitat complexity for energy flow and the maintenance of ecosystem processes in aquatic ecosystems.

Sediments and flow have mainly independent effects on multitrophic stream communities and ecosystem functions

Stream ecosystems are affected by multiple abiotic stressors, and species responses to simultaneous stressors may differ from those predicted based on single-stressor responses. Using 12 semi-natural stream channels, we examined the individual and interactive effects of flow level (low or high flow) and addition of fine sediments (grain size <2 mm) on key ecosystem processes (leaf breakdown, algal biomass accrual) and benthic macroinvertebrate and fungal communities. Both stressors had mostly independent effects on biological responses, with sand addition being the more influential of the two. Sand addition decreased algal biomass and microbe-mediated leaf breakdown significantly, whereas invertebrate shredder-mediated breakdown only responded to flow level. Macroinvertebrate community composition responded significantly to both stressors. Fungal biomass decreased and shredder abundance increased when sand was added; thus, organisms at different trophic levels can exhibit highly variable responses to the same stressor. Terrestrial endophytic fungi were abundant in low-flow flumes where leaf mass loss was also highest, indicating that terrestrial endophytes may contribute importantly to leaf decomposition in the aquatic environment. Leaf breakdown rates depended on the identity and abundance of the dominant decomposer species, suggesting that the effects of anthropogenic activities on ecosystem processes may be driven by changes in the abundance of a few key species. The few observed interactive effects were all antagonistic (i.e., less than the sum of the individual effects); for example, increased flow stimulated algal biomass accumulation but this effect was largely cancelled by sand. While our finding that sand and stream flow did not have strong synergistic effects can be considered reassuring for management, future experiments should manipulate these and other human stressors in experiments that run for much longer periods, thus focusing on the long-term impacts of multiple simultaneously operating stressors.

Quantifying Variability in Four U.S. Streams Using a Long-Term Dataset: Patterns in Biotic Endpoints

Effective water resources assessment and management requires quantitative information on the variability of ambient and biological conditions in aquatic communities. Although it is understood that natural systems are variable, robust estimates of long-term variation in community-based structure and function metrics are rare in U.S. waters. We used a multi-year, seasonally sampled dataset from multiple sites (n = 5-6) in four streams (Codorus Creek, PA; Leaf River, MS; McKenzie and Willamette Rivers, OR) to examine spatial and temporal variation in periphyton chlorophyll a, and fish and macroinvertebrate metrics commonly used in bioassessment programs. Within-site variation of macroinvertebrate metrics and benthic chlorophyll a concentration showed coefficient of variation ranging from 16 to 136%. Scale-specific variability patterns (stream-wide, season, site, and site-season patterns) in standardized biotic endpoints showed that within-site variability patterns extended across sites with variability greatest in chlorophyll a and lowest in Hilsenhoff's Biotic Index. Across streams, variance components models showed that variance attributed to the interaction of space and time and sample variance accounted for the majority of variation in macroinvertebrate metrics and chlorophyll a, while most variation in fish metrics was attributed to sample variance. Clear temporal patterns in measured endpoints were rare and not specific to any one stream or assemblage, while apparent shifts in metric variability related to point source discharges were seen only in McKenzie River macroinvertebrate metrics in the fall. Results from this study demonstrate the need to consider and understand spatial, seasonal, and longer term variability in the development of bioassessment programs and subsequent decisions.

Character displacement and the evolution of niche complementarity in a model biofilm community

Colonization of vacant environments may catalyze adaptive diversification and be followed by competition within the nascent community. How these interactions ultimately stabilize and affect productivity are central problems in evolutionary ecology. Diversity can emerge by character displacement, in which selection favors phenotypes that exploit an alternative resource and reduce competition, or by facilitation, in which organisms change the environment and enable different genotypes or species to become established. We previously developed a model of long-term experimental evolution in which bacteria attach to a plastic bead, form a biofilm, and disperse to a new bead. Here, we focus on the evolution of coexisting mutants within a population of Burkholderia cenocepacia and how their interactions affected productivity. Adaptive mutants initially competed for space, but later competition declined, consistent with character displacement and the predicted effects of the evolved mutations. The community reached a stable equilibrium as each ecotype evolved to inhabit distinct, complementary regions of the biofilm. Interactions among ecotypes ultimately became facilitative and enhanced mixed productivity. Observing the succession of genotypes within niches illuminated changing selective forces within the community, including a fundamental role for genotypes producing small colony variants that underpin chronic infections caused by B. cenocepacia.

Unintended consequences of restoration: loss of riffles and gravel substrates following weir installation

We used pre- and post-restoration channel surveys of the Donner und Blitzen River, Oregon, to evaluate the effects of grade-control structures on channel morphology and baseflow habitat conditions for native redband trout and other aquatic biota. Six years after installation, we found that the channel had a smaller proportion of riffles and pools and less gravel substrate, combined with an increase in the proportion of flat waters and consolidated clay on the bed surface. Both local scour downstream from weirs and backwater effects upstream from weirs appear to have caused the general flattening and fining of the channel. A direct-step backwater calculation indicates that backwaters extended to the upstream weir at both low and high flows, creating long sections of flat water separated by short, steep drops. Despite backwater effects, a comparison of longitudinal profiles before and six years after weir installation showed bed erosion downstream of nearly all weirs, likely a consequence of the cohesive clay material that dominates the channel bed and banks. A deep inner channel reflects the cohesive nature of the clay and the mechanisms of abrasion, and indicates that sediment load is low relative to the transport capacity of the flow. Unfortunately, weirs were problematic in this system because of the cohesive clay substrate, limited sediment supply, and low channel gradient. Although deeper flows due to backwaters might be more favorable for resident trout, less gravel and fewer riffles are likely to negatively impact trout spawning habitat, macroinvertebrate communities, and biofilm productivity. Our results demonstrate the potential limitations of a single-feature approach to restoration that may be ineffective for a given geomorphic context and may overlook other aspects of the ecosystem. We highlight the need to incorporate geomorphic characteristics of a system into project design and predictions of system response.

Evaluation of deposited sediment and macroinvertebrate metrics used to quantify biological response to excessive sedimentation in agricultural streams

The objective of this study was to evaluate which macroinvertebrate and deposited sediment metrics are best for determining effects of excessive sedimentation on stream integrity. Fifteen instream sediment metrics, with the strongest relationship to land cover, were compared to riffle macroinvertebrate metrics in streams ranging across a gradient of land disturbance. Six deposited sediment metrics were strongly related to the relative abundance of Ephemeroptera, Plecoptera and Trichoptera and six were strongly related to the modified family biotic index (MFBI). Few functional feeding groups and habit groups were significantly related to deposited sediment, and this may be related to the focus on riffle, rather than reach-wide macroinvertebrates, as reach-wide sediment metrics were more closely related to human land use. Our results suggest that the coarse-level deposited sediment metric, visual estimate of fines, and the coarse-level biological index, MFBI, may be useful in biomonitoring efforts aimed at determining the impact of anthropogenic sedimentation on stream biotic integrity.

Physical heterogeneity increases biofilm resource use and its molecular diversity in stream mesocosms

BACKGROUND

Evidence increasingly shows that stream ecosystems greatly contribute to global carbon fluxes. This involves a tight coupling between biofilms, the dominant form of microbial life in streams, and dissolved organic carbon (DOC), a very significant pool of organic carbon on Earth. Yet, the interactions between microbial biodiversity and the molecular diversity of resource use are poorly understood.

METHODOLOGY/PRINCIPAL FINDINGS

Using six 40-m-long streamside flumes, we created a gradient of streambed landscapes with increasing spatial flow heterogeneity to assess how physical heterogeneity, inherent to streams, affects biofilm diversity and DOC use. We determined bacterial biodiversity in all six landscapes using 16S-rRNA fingerprinting and measured carbon uptake from glucose and DOC experimentally injected to all six flumes. The diversity of DOC molecules removed from the water was determined from ultrahigh-resolution Fourier Transform Ion Cyclotron Resonance mass spectrometry (FTICR-MS). Bacterial beta diversity, glucose and DOC uptake, and the molecular diversity of DOC use all increased with increasing flow heterogeneity. Causal modeling and path analyses of the experimental data revealed that the uptake of glucose was largely driven by physical processes related to flow heterogeneity, whereas biodiversity effects, such as complementarity, most likely contributed to the enhanced uptake of putatively recalcitrant DOC compounds in the streambeds with higher flow heterogeneity.

CONCLUSIONS/SIGNIFICANCE

Our results suggest biophysical mechanisms, including hydrodynamics and microbial complementarity effects, through which physical heterogeneity induces changes of resource use and carbon fluxes in streams. These findings highlight the importance of fine-scale streambed heterogeneity for microbial biodiversity and ecosystem functioning in streams, where homogenization and loss of habitats increasingly reduce biodiversity.

Fine scale patterns in microbial extracellular enzyme activity during leaf litter decomposition in a stream and its floodplain

Microorganisms mediate the decomposition of leaf-litter through the release of extracellular enzymes. The surfaces of decomposing leaves are both chemically and physically heterogeneous, and spatial patterns in microbial enzyme activity on the litter surface should provide insights into fine-scale patterns of leaf-litter decomposition. Platanus occidentalis leaves were collected from the floodplain of a third-order stream in northern Mississippi, enclosed in individual litter bags, and placed in the stream channel and in the floodplain. Replicate leaves were collected approximately monthly over a 9-month period and assayed for spatial variation in microbial extracellular enzyme activity and rates of organic matter (OM) decomposition. Spatial variation in enzyme activity was measured by sampling 96 small discs (5-mm diameter) cut from each leaf. Discs were assayed for the activity of enzymes involved in lignin (oxidative enzymes) and cellulose (beta-glucosidase, cellobiohydrolase) degradation. Rates of OM loss were greater in the stream than the floodplain. Activities of all enzymes displayed high variability in both environments, with severalfold differences across individual leaves, and replicate leaves varied greatly in their distribution of activities. Geostatistical analysis revealed no clear patterns in spatial distribution of activity over time or among replicates, and replicate leaves were highly variable. These results show that fine-scale spatial heterogeneity occurs on decomposing leaves, but the level of spatial variability varies among individual leaves at the measured spatial scales. This study is the first to use geostatistical analyses to analyze landscape patterns of microbial activity on decomposing leaf litter and in conjunction with studies of the microbial community composition and/or substrate characteristics, should provide key insights into the function of these processes.

Bacterial community composition of stream biofilms in spatially variable-flow environments

Streams are highly heterogeneous ecosystems, in terms of both geomorphology and hydrodynamics. While flow is recognized to shape the physical architecture of benthic biofilms, we do not yet understand what drives community assembly and biodiversity of benthic biofilms in the heterogeneous flow landscapes of streams. Within a metacommunity ecology framework, we experimented with streambed landscapes constructed from bedforms in large-scale flumes to illuminate the role of spatial flow heterogeneity in biofilm community composition and biodiversity in streams. Our results show that the spatial variation of hydrodynamics explained a remarkable percentage (up to 47%) of the variation in community composition along bedforms. This suggests species sorting as a model of metacommunity dynamics in stream biofilms, though natural biofilm communities will clearly not conform to a single model offered by metacommunity ecology. The spatial variation induced by the hydrodynamics along the bedforms resulted in a gradient of bacterial beta diversity, measured by a range of diversity and similarity indices, that increased with bedform height and hence with spatial flow heterogeneity at the flume level. Our results underscore the necessity to maintain small-scale physical heterogeneity for community composition and biodiversity of biofilms in stream ecosystems.

Imaging oxygen distribution in marine sediments. The importance of bioturbation and sediment heterogeneity

The influence of sediment oxygen heterogeneity, due to bioturbation, on diffusive oxygen flux was investigated. Laboratory experiments were carried out with 3 macrobenthic species presenting different bioturbation behaviour patterns: the polychaetes Nereis diversicolor and Nereis virens, both constructing ventilated galleries in the sediment column, and the gastropod Cyclope neritea, a burrowing species which does not build any structure. Oxygen two-dimensional distribution in sediments was quantified by means of the optical planar optode technique. Diffusive oxygen fluxes (mean and integrated) and a variability index were calculated on the captured oxygen images. All species increased sediment oxygen heterogeneity compared to the controls without animals. This was particularly noticeable with the polychaetes because of the construction of more or less complex burrows. Integrated diffusive oxygen flux increased with oxygen heterogeneity due to the production of interface available for solute exchanges between overlying water and sediments. This work shows that sediment heterogeneity is an important feature of the control of oxygen exchanges at the sediment-water interface.

Grazing regulates the spatial variability of periphyton biomass

The presence of consumers not only alters the mean biomass of the prey assemblage, but also affects the spatial heterogeneity of biomass distribution. Whereas the mean prey biomass is generally reduced by consumer presence, the effect on spatial heterogeneity is less clear-cut. A meta-analysis of almost 600 field experiments manipulating the presence of benthic invertebrate or vertebrate grazers was conducted to analyze the effect of grazers on both the absolute spatial variability of periphyton biomass and the relative variability, which was standardized to the mean. Effects on absolute variability were measured as the log response ratio of the standard deviation of biomass (LR-SD), whereas effects on relative variability were measured as the log response ratio of the coefficient of variation of biomass (LR-CV). The overall magnitude and range of LR-SD and LR-CV indicated that grazers not only reduced periphyton biomass, but also substantially altered their spatial distribution. However, grazer effects differed strongly for absolute and relative variability. On average, grazers reduced the absolute spatial variability in prey biomass by 50% (average LR-SD = -0.68) but increased the relative variability by 24% (average LR-CV = 0.22). The magnitude of LR-SD strongly depended on the efficiency of grazing, with strong biomass removal leading to strong homogenization. Moreover, LR-CV and LR-SD were significantly affected by habitat type (freshwater vs. coastal) and substrata. Given the importance of spatial heterogeneity for resource uptake, competition and the maintenance of diversity, grazer presence has potentially strong indirect effects on the interactions within prey assemblages.

A flow-lane incubator for studying freshwater and marine phototrophic biofilms

Phototrophic biofilms are defined as interfacial microbial communities mainly driven by light as energy source and are studied for both ecological and technological reasons. Field investigations of biofilms usually do not offer the opportunity to study the effects of a large number of external parameters. In order to investigate the temporal development of phototrophic communities a laboratory flow-lane incubator for cultivation of freshwater and marine biofilms was developed. The incubator has four lanes which accommodate microscope slides used as substratum and for sampling. The slides can be of different material and may be employed for characterisation of phototrophic biofilms by means of gravimetry, microscopy, taxonomy, molecular biology and chemical analysis. The design allows control of irradiance, temperature and flow velocity. Furthermore, on-line control of biomass accumulation via specially adapted light sensors was proved to be a suitable indicator of temporal developmental stages (initial adhesion, active growth and mature stage). Spatial heterogeneity of the cultivated phototrophic biofilms along the flow direction within each flow-lane was low. Biofilm growth characteristics (e. g. lag time, net accrual rate, peak biomass) recorded in dependency from external conditions may be used as input data for training of artificial neural networks (ANN) and mechanistic modelling. The material and devices used in combination with low maintenance costs and ease of handling suggests the flow-lane incubator as a useful tool for studying the influence of abiotic and biotic factors on the development of freshwater and marine phototrophic biofilms.

Temporal variance reverses the impact of high mean intensity of stress in climate change experiments

Extreme climate events produce simultaneous changes to the mean and to the variance of climatic variables over ecological time scales. While several studies have investigated how ecological systems respond to changes in mean values of climate variables, the combined effects of mean and variance are poorly understood. We examined the response of low-shore assemblages of algae and invertebrates of rocky seashores in the northwest Mediterranean to factorial manipulations of mean intensity and temporal variance of aerial exposure, a type of disturbance whose intensity and temporal patterning of occurrence are predicted to change with changing climate conditions. Effects of variance were often in the opposite direction of those elicited by changes in the mean. Increasing aerial exposure at regular intervals had negative effects both on diversity of assemblages and on percent cover of filamentous and coarsely branched algae, but greater temporal variance drastically reduced these effects. The opposite was observed for the abundance of barnacles and encrusting coralline algae, where high temporal variance of aerial exposure either reversed a positive effect of mean intensity (barnacles) or caused a negative effect that did not occur under low temporal variance (encrusting algae). These results provide the first experimental evidence that changes in mean intensity and temporal variance of climatic variables affect natural assemblages of species interactively, suggesting that high temporal variance may mitigate the ecological impacts of ongoing and predicted climate changes.

TEMPORAL VARIANCE REVERSES THE IMPACT OF HIGH MEAN INTENSITY OF STRESS IN CLIMATE CHANGE EXPERIMENTS

Extreme climate events produce simultaneous changes to the mean and to the variance of climatic variables over ecological time scales. While several studies have investigated how ecological systems respond to changes in mean values of climate variables, the combined effects of mean and variance are poorly understood. We examined the response of low-shore assemblages of algae and invertebrates of rocky seashores in the northwest Mediterranean to factorial manipulations of mean intensity and temporal variance of aerial exposure, a type of disturbance whose intensity and temporal patterning of occurrence are predicted to change with changing climate conditions. Effects of variance were often in the opposite direction of those elicited by changes in the mean. Increasing aerial exposure at regular intervals had negative effects both on diversity of assemblages and on percent cover of filamentous and coarsely branched algae, but greater temporal variance drastically reduced these effects. The opposite was observed for the abundance of barnacles and encrusting coralline algae, where high temporal variance of aerial exposure either reversed a positive effect of mean intensity (barnacles) or caused a negative effect that did not occur under low temporal variance (encrusting algae). These results provide the first experimental evidence that changes in mean intensity and temporal variance of climatic variables affect natural assemblages of species interactively, suggesting that high temporal variance may mitigate the ecological impacts of ongoing and predicted climate changes.

Global production increased by spatial heterogeneity in a population dynamics model

Spatial and temporal heterogeneity are often described as important factors having a strong impact on biodiversity. The effect of heterogeneity is in most cases analyzed by the response of biotic interactions such as competition of predation. It may also modify intrinsic population properties such as growth rate. Most of the studies are theoretic since it is often difficult to manipulate spatial heterogeneity in practice. Despite the large number of studies dealing with this topics, it is still difficult to understand how the heterogeneity affects populations dynamics. On the basis of a very simple model, this paper aims to explicitly provide a simple mechanism which can explain why spatial heterogeneity may be a favorable factor for production. We consider a two patch model and a logistic growth is assumed on each patch. A general condition on the migration rates and the local subpopulation growth rates is provided under which the total carrying capacity is higher than the sum of the local carrying capacities, which is not intuitive. As we illustrate, this result is robust under stochastic perturbations.

Experimental evaluation of early patterns of colonisation of space on rocky shores and seawalls

The introduction of artificial structures in coastal areas can cause fragmentation and loss of natural habitats. Previous studies found that variation in colonisation of space at mid-shore levels could account for differences in mature assemblages between seawalls and vertical surfaces on adjacent rocky shores in Sydney Harbour (Australia). This study tests the model that the nature of the substratum is responsible for different patterns of early colonisation between vertical ledges of rocky shores and seawalls. According to this model, patterns in early colonisation would differ between cleared areas created on vertical surfaces on rocky shores and seawalls, but not between standard surfaces (panels) installed on each structure. Early colonisation of space differed between seawalls and rocky shores, regardless of the type of substratum (clearings versus panels). Differences in relative abundances between structures were evident on both types of substrata for some taxa, while they varied between substrata for others. No taxa, however, showed consistent differences between structures in only the clearings. In addition, the abundance of some taxa differed between panels on the different structures, suggesting that the effects of the substratum were modulated by factors operating differentially between rocky shores and seawalls.