Habitat coupling in lake ecosystems

Lakes are complex ecosystems composed of distinct habitats coupled by biological, physical and chemical processes. While the ecological and evolutionary characteristics of aquatic organisms reflect habitat coupling in lakes, aquatic ecology has largely studied pelagic, benthic and riparian habitats in isolation from each other. Here, we summarize several ecological and evolutionary patterns that highlight the importance of habitat coupling and discuss their implications for understanding ecosystem processes in lakes. We pay special attention to fishes because they play particularly important roles as habitat couplers as a result of their high mobility and flexible foraging tactics that lead to inter-habitat omnivory. Habitat coupling has important consequences for nutrient cycling, predator-prey interactions, and food web structure and stability. For example, nutrient excretion by benthivorous consumers can account for a substantial fraction of inputs to pelagic nutrient cycles. Benthic resources also subsidize carnivore populations that have important predatory effects on plankton communities. These benthic subsidies stabilize population dynamics of pelagic carnivores and intensify the strength of their interactions with planktonic food webs. Furthermore, anthropogenic disturbances such as eutrophication, habitat modification, and exotic species introductions may severely alter habitat connections and, therefore, the fundamental flows of nutrients and energy in lake ecosystems.     

Habitat use,but not gene flow,is influenced by human activities in two ecotypes of Egyptian fruit bat (Rousettus aegyptiacus)

Understanding the ecological, behavioural and evolutionary response of organisms to changing environments is of primary importance in a human‐altered world. It is crucial to elucidate how human activities alter gene flow and what are the consequences for the genetic structure of a species. We studied two lineages of the Egyptian fruit bat (Rousettus aegyptiacus) throughout the contact zone between mesic and arid Ecozones in the Middle East to evaluate the species' response to the growing proportion of human‐altered habitats in the desert. We integrated population genetics, morphometrics and movement ecology to analyse population structure, morphological variation and habitat use from GPS‐ or radio‐tagged individuals from both desert and Mediterranean areas. We classified the spatial distribution and environmental stratification by describing physical–geographical conditions and land cover. We analysed this information to estimate patch occupancy and used an isolation‐by‐resistance approach to model gene flow patterns. Our results suggest that lineages from desert and Mediterranean habitats, despite their admixture, are isolated by environment and by adaptation supporting their classification as ecotypes. We found a positive effect of human‐altered habitats on patch occupancy and habitat use of fruit bats by increasing the availability of roosting and foraging areas. While this commensalism promotes the distribution of fruit bats throughout the Middle East, gene flow between colonies has not been altered by human activities. This discrepancy between habitat use and gene flow patterns may, therefore, be explained by the breeding system of the species and modifications of natal dispersal patterns.     

The broad-scale distribution of five jellyfish species across a temperate coastal environment

Jellyfish (medusae) are sometimes the most noticeable and abundant members of coastal planktonic communities, yet ironically, this high conspicuousness is not reflected in our overall understanding of their spatial distributions across large expanses of water. Here, we set out to elucidate the spatial (and temporal) patterns for five jellyfish species (Phylum Cnidaria, Orders Rhizostomeae and Semaeostomeae) across the Irish & Celtic Seas, an extensive shelf-sea area at Europe’s northwesterly margin encompassing several thousand square kilometers. Data were gathered using two independent methods: (1) surface-counts of jellyfish from ships of opportunity, and (2) regular shoreline surveys for stranding events over three consecutive years. Jellyfish species displayed distinct species-specific distributions, with an apparent segregation of some species. Furthermore, a different species composition was noticeable between the northern and southern parts of the study area. Most importantly, our data suggests that jellyfish distributions broadly reflect the major hydrographic regimes (and associated physical discontinuities) of the study area, with mixed water masses possibly acting as a trophic barrier or non-favourable environment for the successful growth and reproduction of jellyfish species. Handling Editor: K. Martens     

Spatial and genetic investigation of aggregation in Ischnochiton (Polyplacophora; Neoloricata; Ischnochitonina; Ischnochitonidae; Ischnochitoninae) species with different larval development

Many species are aggregated at some spatial scale but for some species, due to habitat or behaviour, aggregation can be difficult to assess quantitatively. Here, aggregation of chiton species (Polyplacophora; Neoloricata; Ischnochitonina; Ischnochitonidae; Ischnochitoninae; Ischnochiton) living under boulders in intertidal boulder fields was investigated at several relatively small spatial scales. Closely related species were found to be aggregated at the level of individual boulders, but evidence for grouping at the larger scale of patches of boulders varied. When organisms are mobile, dispersal can have an important influence on spatial patterns. Some organisms, such as marine invertebrates, have a highly dispersive larval phase that can influence spatial patterns of adults, particularly where the adult is sessile or relatively sedentary. Aggregation was compared in two species to test whether different modes of larval development influence spatial pattern. There was some evidence that species with a planktonic larva were even more aggregated than expected, in contrast to predictions based on this mode of development. Both types of larval development (planktonic and non‐planktonic) produce larvae with short development times in these species, so one possible explanation for the grouping habit of these chitons is that they do not disperse, at all, from their natal boulder. The complexity of the boulder field habitat and the cryptic behaviour of these chitons may also contribute to a lack of dispersal. A simple application of a genetic method indicated, however, that philopatry at this scale is unlikely.     

Non-indigenous invasive bivalves as ecosystem engineers

Several non-indigenous bivalve species have been colonising aquatic ecosystems worldwide, in some cases with great ecological and economic impacts. In this paper, we focus on the ecosystem engineering attributes of non-indigenous invasive bivalves (i.e., the capacities of these organisms to directly or indirectly affect the availability of resources to other species by physically modifying the environment). By reviewing the ecology of several invasive bivalves we identify a variety of mechanisms via which they modify, maintain and/or create habitats. Given the usually high densities and broad spatial distributions of such bivalves, their engineering activities can significantly alter ecosystem structure and functioning (e.g., changes in sediment chemistry, grain size, and organic matter content via bioturbation, increased light penetration into the water column due to filter feeding, changes in near bed flows and shear stress due to the presence of shells, provision of colonisable substrate and refuges by shells). In addition, changes in ecosystem structure and functioning due to engineering by invasive bivalves often have very large economic impacts. Given the worldwide spread of non-indigenous bivalves and the varied ways in which they physically modify habitats, their engineering effects should receive more serious consideration in restoration and management initiatives.     

Metacommunities of spiders in grassland habitat fragments of an agricultural landscape

Arthropod communities in fragmented agricultural landscapes depend on local processes and the interactions between communities in the habitat islands. We aimed to study metacommunity structure of spiders, a group that is known for high dispersal power, local niche partitioning and for engaging in species interactions. While living in fragmented habitats could lead to nestedness, other ecological traits of spiders might equally lead to patterns dominated either by species interactions or habitat filtering. We asked, which community pattern will prevail in a typical agricultural landscape with isolated patches of semi-natural habitats. Such a situation was studied by sampling spiders in 28 grassland locations in a Hungarian agricultural landscape. We used the elements of metacommunity structure (EMS) framework to distinguish between alternative patterns that reveal community organization. The EMS analysis indicated coherent species ranges, high turnover and boundary clumping, suggesting Clementsian community organization. The greatest variation in species composition was explained by local habitat characteristics, indicating habitat filtering. The influence of dispersal could be detected by the significant effect of landscape composition, which was strongest at 500 m. We conclude that dispersal allows spiders to respond coherently to the environment, creating similar communities in similar habitats. Consistent habitat differences, such as species rich versus species poor vegetation, lead to recognisably different, recurrent communities. These characteristics make spiders a predictable and diverse source of natural enemies in agricultural landscapes. Sensitivity to habitat composition at medium distances warns us that landscape homogenization may alter these metacommunity processes.     

The effect of habitat structure on prey mortality depends on predator and prey microhabitat use

Structurally complex habitats provide cover and may hinder the movement of animals. In predator–prey relationships, habitat structure can decrease predation risk when it provides refuges for prey or hinders foraging activity of predators. However, it may also provide shelter, supporting structures and perches for sit-and-wait predators and hence increase their predation rates. We tested the effect of habitat structure on prey mortality in aquatic invertebrates in short-term laboratory predation trials that differed in the presence or absence of artificial vegetation. The effect of habitat structure on prey mortality was context dependent as it changed with predator and prey microhabitat use. Specifically, we observed an ‘anti-refuge’ effect of added vegetation: phytophilous predators that perched on the plants imposed higher predation pressure on planktonic prey, while mortality of benthic prey decreased. Predation by benthic and planktonic predators on either type of prey remained unaffected by the presence of vegetation. Our results show that the effects of habitat structure on predator–prey interactions are more complex than simply providing prey refuges or cover for predators. Such context-specific effects of habitat complexity may alter the coupling of different parts of the ecosystem, such as pelagic and benthic habitats, and ultimately affect food web stability through cascading effects on individual life histories and trophic link strengths.     

Habitat structure,conspecific presence and spatial variation in the recruitment of a temperate reef fish

Pronounced spatial variation in recruitment occurs in many marine invertebrate and fish populations and is thought to be critical to the demography of these species. In this study I examined the importance of habitat structure and the presence of conspecific residents to spatial variation in larval settlement and recruitment in a temperate fish Tautogolabrus adspersus. I define settlement as the movement of individuals from the water column to the benthic habitat, while I refer to recruitment as numbers of individuals surviving some arbitrary period of time after settlement. Experiments in which standard habitats were stocked with conspecifics showed that resident conspecifics were not an important factor contributing to small-scale variability in recruitment. Further correlative analyses demonstrated that large-scale variation in recruitment could not be explained by variability in older age classes. By contrast, manipulations of macroalgal structure within a kelp bed demonstrated that recruitment was significantly higher in habitats with a dense understory of foliose and filamentous algae than in habitats with only crustose algae. Understory algae varied in their pattern of disperison among sites, and the dispersion of fish matched that of the plants. In order to determine the effects of differences in patterns of algal dispersion on the demography of associated T. adspersus populations, I used experimental habitat units to manipulate patterns of dispersion. Settlement was significantly greater to randomly placed versus clumped habitats; however, no differences in recruitment between random and clumped habitats were detected. Because recruitment is a function of the numbers of settlers minus the subsequent loss of settlers, rates of mortality or migration must have been higher in the randomly placed habitats. These results are counter to the current paradigm for reef fishes which suggests that larval settlement is the crucial demographic process producing variability in population abundance. In this experiment patterns of settlement were modified by varying the patch structure of the habitat.Contribution number 278 from the Center for Marine Biology, University of New Hampshire     

Monitoring program design for data‐limited marine biogenic habitats: A structured approach

Marine biogenic habitats—habitats created by living organisms—provide essential ecosystem functions and services, such as physical structuring, nutrient cycling, biodiversity support, and increases in primary, secondary, and tertiary production. With the growing trend toward ecosystem approaches to marine conservation and fisheries management, there is greater emphasis on rigorously designed habitat monitoring programs. However, such programs are challenging to design for data‐limited habitats for which underlying ecosystem processes are poorly understood. To provide guidance in this area, we reviewed approaches to benthic assessments across well‐studied marine biogenic habitats and identified common themes related to indicator selection, sampling methods, and survey design. Biogenic habitat monitoring efforts largely focus on the characteristics, distribution, and ecological function of foundation species, but may target other habitat‐forming organisms, especially when community shifts are observed or expected, as well as proxies of habitat status, such as indicator species. Broad‐scale methods cover large spatial areas and are typically used to examine the spatial configuration of habitats, whereas fine‐scale methods tend to be laborious and thus restricted to small survey areas, but provide high‐resolution data. Recent, emerging methods enhance the capabilities of surveying large areas at high spatial resolution and improve data processing efficiency, bridging the gap between broad‐ and fine‐scale methods. Although sampling design selection may be limited by habitat characteristics and available resources, it is critically important to ensure appropriate matching of ecological, observational, and analytical scales. Drawing on these common themes, we propose a structured, iterative approach to designing monitoring programs for marine biogenic habitats that allows for rigorous data collection to inform management strategies, even when data and resource limitations are present. A practical application of this approach is illustrated using glass sponge reefs—a recently discovered and data‐limited habitat type—as a case study.     

Ecological traps and species distribution models: a challenge for prioritizing areas of conservation importance

Species distribution models analyse how species use different types of habitats. Their spatial predictions are often used to prioritize areas for conservation. Individuals may, however, prefer settling in habitat types of low quality compared to other available habitats. This ecological trap phenomenon is usually studied in a small number of habitat patches and consequences at the landscape level are largely unknown. It is therefore often unclear whether the spatial pattern of habitat use is aligned with the behavioural decisions made by the individuals during habitat selection or reflects actual variation in the quality of different habitat types. As species distribution models analyse the pattern of occurrence in different habitats, there is a conservation interest in examining what their predictions mean in terms of habitat quality when ecological traps are operating. Previous work in Belgium showed that red-backed shrikes Lanius collurio are more attracted to newly available clear-cut habitat in plantation forests than to the traditionally used farmland habitat. We developed models with shrike distribution data and compared their predictions with spatial variation in shrike reproductive performance used as a proxy for habitat quality. Models accurately predicted shrike distribution and identified the preferred clear-cut patches as the most frequently used habitat, but reproductive performance was lower in clear-cut areas than in farmland. With human-induced rapid environmental changes, organisms may indeed be attracted to low-quality habitats and occupy them at high densities. Consequently, the predictions of statistical models based on occurrence records may not align with variation in significant population parameters for the maintenance of the species. When species expand their range to novel habitats, such models are useful to document the spatial distribution of the organisms, but data on population growth rates are worth collecting before using model predictions to guide the spatial prioritization of conservation actions.     

Spatial distribution of the upside-down jellyfish Cassiopea sp. within fringing coral reef environments of the Northern Red Sea: implications for its life cycle

The zooxanthellate mangrove jellyfish Cassiopea sp. represents a prominent invasive species and a potential bioindicator for nutrient monitoring in coral reefs. However, information about its spatial distribution in combination with abundance, habitat specificity and life cycle elements is barely available. This study, therefore, presents the results of field surveys conducted within four different benthic habitat types (coral reef, seagrass meadow, reef-sand transition and sand flat) in the Northern Red Sea. Cassiopea sp. exhibited a highly patchy distribution within the entire study area with mean abundance of 1.6 ± 0.3 animals m⁻² and benthic coverage of 3.2%. Within coral reef habitats, maximum abundance of up to 31 animals m⁻² and benthic coverage of up to 20% were detected. Additionally, this study revealed that 65% of all observed Cassiopea specimens were associated with the commensalistic crustacean mysid Idiomysis tsurnamali. Cassiopea abundance and size as well as association patterns with mysids differed between most of the surveyed habitats. In summary, the findings of the present study (1) characterize Cassiopea as one of the key organisms in investigated benthic habitats, (2) indicate active habitat selection by the jellyfish and (3) may hint to an unexplored life cycle of Cassiopea with central role of seagrass meadows providing cues for larval settlement and metamorphosis in the absence of mangroves.     

Conditional responses of organisms to habitat structure: an example from intertidal mudflats

Habitat structure is often assumed to be a predictor of habitat function. However, habitat structure may be insufficient to predict the functional significance of a habitat if the level of resources in the habitat is a consequence of the interaction between the habitat structure and physical or biological factors. In this study, we investigated whether depressions in tidal flat sediments generated by stout razor clams, Tagelus plebeius, affect the spatial patterns of pit digging by deposit-feeding burrowing crabs, Chasmagnathus granulata. The pits dug by crabs while feeding overlapped with clam siphon holes at a frequency higher than expected at random, and measurements of pit-digging by crabs integrated over several days indicated a higher frequency of feeding in the sediment of depressions. The daily frequency of pit-digging by crabs in depressions was positively related to the organic matter content of their sediments, but was significantly higher than the frequency of pit-digging away from clam siphon holes only after events of high bedload sediment transport, when the organic matter in the sediments of these depressions peaked. This example demonstrates the conditional nature of the relationship between habitat structure and function by illustrating how a physical process—bedload sediment transport—may introduce variation in the function that depressions play as feeding sites for burrowing crabs. Published information suggests that such conditional responses of organisms to habitat structure: (1) occur in a variety of habitats; (2) involve a variety of structures either of biotic or abiotic origin; and (3) are the consequence of either physical or biological controls that vary in importance according to the general mechanism through which habitat structure affect resources. This broad experimental evidence suggests that the accuracy of predictive models linking habitat structure and function can be improved by incorporating a mechanistic perspective that allows recognition of the potential for conditional responses of organisms to habitat structure.     

Spatial autocorrelation and dispersal limitation in freshwater organisms

Dispersal can limit the ranges of species and the diversity of communities. Despite its importance, little is known about its role in freshwater habitats and its relation to habitat type (lentic vs. lotic), especially for organisms with cryptic dispersal methods such as plankton. Poor dispersers are expected to show more clumped distributions or greater spatial autocorrelation (SA) in community composition than good dispersers. We examined patterns of SA across freshwater taxa with different dispersal modes (active vs. passive) and their association with habitat type (lake vs. stream) using 18 spatially explicit community composition data sets. We found significant relationships between SA and body size among taxa in lake habitats, but not in streams. However, the increase in SA with body size in lakes was driven entirely by fishes—organisms ranging in size from diatoms to macro-invertebrates showed equivalent levels of SA. These results support the idea that large organisms are less effective dispersers in aquatic environments, resulting in greater SA in community structure over broad scales. Streams may be effectively more connected than lakes as patterns of SA and body size were weaker in lotic habitats. Our data suggest that the critical threshold where greater body size increases dispersal limitation seems to come at the juncture between invertebrates and vertebrates rather than that between unicellular and multicellular organisms as has been previously suggested. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Stream flow alone does not predict population structure of diving beetles across complex tropical landscapes

Recent theoretical advances have hypothesized a central role of habitat persistence on population genetic structure and resulting biodiversity patterns of freshwater organisms. Here, we address the hypothesis that lotic species, or lineages adapted to comparably geologically stable running water habitats (streams and their marginal habitats), have high levels of endemicity and phylogeographic structure due to the persistent nature of their habitat. We use a nextRAD DNA sequencing approach to investigate the population structure and phylogeography of a putatively widespread New Guinean species of diving beetle, Philaccolilus ameliae (Dytiscidae). We find that P. ameliae is a complex of morphologically cryptic, but geographically and genetically well‐differentiated clades. The pattern of population connectivity is consistent with theoretical predictions associated with stable lotic habitats. However, in two clades, we find a more complex pattern of low population differentiation, revealing dispersal across rugged mountains and watersheds of New Guinea up to 430 km apart. These results, while surprising, were also consistent with the original formulation of the habitat template concept by Southwood, involving lineage‐idiosyncratic evolution in response to abiotic factors. In our system, low population differentiation might reflect a young species in a phase of range expansion utilizing vast available habitat. We suggest that predictions of life history variation resulting from the dichotomy between lotic and lentic organisms require more attention to habitat characterization and microhabitat choice. Our results also underpin the necessity to study fine‐scale processes but at a larger geographical scale, as compared to solely documenting macroecological patterns, to understand ecological drivers of regional biodiversity. Comprehensive sampling especially of tropical lineages in complex and threatened environments such as New Guinea remains a critical challenge.     

Interstitial Ciliates: Benthic Microaerophiles or Planktonic Anaerobes?

We observed marine benthic interstitial ciliates Geleia sp. and Tracheloraphis sp. inhabiting the water column of a chemically stratified salt pond. This habitat is uncharacteristic for interstitial ciliates, yet they displayed active and abundant planktonic populations (up to 800 and 250 cells/liter, respectively) and a well-defined pattern of vertical distribution. Completely absent from the oxygenated epilimnion, they first appeared at the oxic/anoxic interface and were present throughout the anoxic hypolimnion. The data could not be explained by a passive removal (e.g. by currents) of these ciliates from their conventional habitat (soft sediments) to water column. The results suggest that 1) these ciliates favored an anoxic environment, and 2) they switched to a planktonic lifestyle as appropriate conditions (seasonal anoxia) developed in the water column. This sharply contrasts the classic view of these ciliates as specifically benthic and aerobic (albeit microaerophilic) organisms. We hypothesize that Geleia sp. and Tracheloraphis sp. can readily grow in either water column or benthos, but are typically found in sediments simply because they contain their preferred (anoxic) niche.     

Scale dependent diversity patterns in arboreal and terrestrial oribatid mite (Acari: Oribatida) communities

In naturally fragmented, isolated, or patchily distributed habitats that contain non‐vagile organisms, we expect dispersal to be limited, and patterns of diversity to differ from similar, yet continuous habitats. We explored the alpha‐beta‐gamma relationship and community composition of oribatid mites (Acari: Oribatida) inhabiting spatially discrete canopy suspended soils, and compared the patterns of diversity with the continuous forest floor soils over two years. We explored dispersal limitation for oribatid mites in the canopy by using additive partitioning of species richness at multiple spatial scales. ANOSIM was used to demonstrate differences in oribatid mite community composition between the canopy and forest floor habitats over different sampling periods. Community composition of oribatid mites differed significantly between canopy and forest floor habitats, by season and yearly sampling period. Oribatid mite richness and abundance were positively correlated with substrate moisture content, particularly in the canopy. Richness and abundance of ground oribatid mites was greater in September than in June, a trend that is reversed in the canopy, suggesting canopy oribatid mite species may have altered life histories to take advantage of earlier moisture conditions. Alpha diversity of oribatid mites in the canopy was lower than the ground at all sampling levels, and not significantly different from a random distribution in either habitat. Beta diversity was greater than expected from a random distribution at the patch‐ and tree‐level in the canopy suggesting dispersal limitation associated with physical tree‐to‐tree dispersal barriers, and limited dispersal among patches within a tree. Beta diversity at the tree‐level was the largest contribution to overall species richness in both canopy and ground habitats, and was also greater than expected on the ground. These results suggest that factors other than physical dispersal barriers, such as aggregation, habitat availability, and environmental factors (moisture), may limit the distribution of species in both habitats.     

Factors shaping the range-size frequency distribution of the endemic fish fauna of the Tropical Eastern Pacific

Aim To assess the effect of habitat fragmentation and isolation in determining the range‐size frequency distribution (RFD) of the shorefish fauna endemic to a discrete biogeographical region. Location The Tropical Eastern Pacific (TEP). Methods Habitat isolation represents the separation between oceanic islands and the continental shore of the TEP and habitat fragmentation the degree of spatial continuity of habitats (i.e. reefs, soft bottom, nearshore waters) along the continental coast of the TEP. The effects of habitat isolation and fragmentation were quantified by comparing the RFDs of (1) the species found on oceanic islands vs. the continental shore, and (2) species on the continental shore that use different habitat types. Results The RFD of the entire TEP fauna was bimodal, with peaks at both small‐ and large‐range ends of the spectrum. The small‐range peak was due almost entirely to island species and the large‐range peak due mainly to species found in both the continental shore and oceanic islands. RFDs varied among species using different habitats on the continental shore: reef‐fishes had a right‐skewed RFD, soft‐bottom species a flat RFD, and coastal‐pelagic fishes a left‐skewed RFD. Main conclusions Variation in dispersal capabilities associated with habitat isolation and fragmentation in the TEP appears to be the main mechanism contributing to differences among RFD structure, although variation in tolerances arising from the dynamic regional environment may contribute to some patterns. Because diversity patterns are strongly affected by RFD structure, it is now evident that the insular and continental components of a fauna should be treated separately when analysing such patterns. Furthermore, contrasts in RFD structure among species using different habitats demonstrate that a full understanding of the causes of diversity patterns requires analyses of complete regional faunas in relation to regional geography.     

Habitat use by a Midwestern U.S.A. riverine fish assemblage: effects of season, water temperature and river discharge

The hypothesis that temperate stream fishes alter habitat use in response to changing water temperature and stream discharge was evaluated over a 1 year period in the Neosho River, Kansas, U.S.A. at two spatial scales. Winter patterns differed from those of all other seasons, with shallower water used less frequently, and low‐flow habitat more frequently, than at other times. Non‐random habitat use was more frequent at the point scale (4·5 m²) than at the larger reach scale (20–40 m), although patterns at both scales were similar. Relative to available habitats, assemblages used shallower, swifter‐flowing water as temperature increased, and shallower, slower‐flowing water as river discharge increased. River discharge had a stronger effect on assemblage habitat use than water temperature. Proportion of juveniles in the assemblage did not have a significant effect. This study suggests that many riverine fishes shift habitats in response to changing environmental conditions, and supports, at the assemblage level, the paradigm of lotic fishes switching from shallower, high‐velocity habitats in summer to deeper, low‐velocity habitats in winter, and of using shallower, low‐velocity habitats during periods of high discharge. Results also indicate that different species within temperate river fish assemblages show similar habitat use patterns at multiple scales in response to environmental gradients, but that non‐random use of available habitats is more frequent at small scales.