Non‐reef habitats in a tropical seascape affect density and biomass of fishes on coral reefs

Nonreef habitats such as mangroves, seagrass, and macroalgal beds are important for foraging, spawning, and as nursery habitat for some coral reef fishes. The spatial configuration of nonreef habitats adjacent to coral reefs can therefore have a substantial influence on the distribution and composition of reef fish. We investigate how different habitats in a tropical seascape in the Philippines influence the presence, density, and biomass of coral reef fishes to understand the relative importance of different habitats across various spatial scales. A detailed seascape map generated from satellite imagery was combined with field surveys of fish and benthic habitat on coral reefs. We then compared the relative importance of local reef (within coral reef) and adjacent habitat (habitats in the surrounding seascape) variables for coral reef fishes. Overall, adjacent habitat variables were as important as local reef variables in explaining reef fish density and biomass, despite being fewer in number in final models. For adult and juvenile wrasses (Labridae), and juveniles of some parrotfish taxa (Chlorurus), adjacent habitat was more important in explaining fish density and biomass. Notably, wrasses were positively influenced by the amount of sand and macroalgae in the adjacent seascape. Adjacent habitat metrics with the highest relative importance were sand (positive), macroalgae (positive), and mangrove habitats (negative), and fish responses to these metrics were consistent across fish groups evaluated. The 500‐m spatial scale was selected most often in models for seascape variables. Local coral reef variables with the greatest importance were percent cover of live coral (positive), sand (negative), and macroalgae (mixed). Incorporating spatial metrics that describe the surrounding seascape will capture more holistic patterns of fish–habitat relationships on reefs. This is important in regions where protection of reef fish habitat is an integral part of fisheries management but where protection of nonreef habitats is often overlooked.     

Exploratory multiscale analysis of the fish assemblages and habitats of the lower St. Lawrence River,Québec,Canada

This work presents a multiscale analysis of the fish diversity of the lower St. Lawrence River which flows from the Laurentian Great Lakes of North America. A database of about 14,000 fish sampling stations from the lower St. Lawrence is linked to five different habitat maps of the study area: hydrographical units, water masses, depth, sediment type and wetland type. We hypothesize that species turnover (beta diversity) will be significant among these habitat maps. For each map, we calculate a UPGMA dendrogram based on the Jaccard coefficient of similarity in species occurrences as a first assemblage–habitat model. A randomization test is then used to identify the significant dendrograms from which we infer fish assemblages. We then show that many species are actually selecting or avoiding habitats. Finally, species selecting particular habitats are described by some selected ecological traits that are expected to occur frequently in those habitats. We found assemblages for the hydrographical units but not for the water masses. The fluvial section is selected by many stenohaline and some euryhaline species, while the freshwater estuary and the brackish estuary are only selected by euryhaline species. In the fluvial section at the hydrographical unit scale, many species associated with lentic habitats are limnophilic and more vegetation-dependent while many species selecting lotic habitats are rheophilic insectivorous species. Significant assemblages are defined for depth, sediment type and wetland type. Taken together, we found strong empirical evidence of a diverse actively selecting littoral assemblage of small, low mobility fishes opposing a channel assemblage of larger, more mobile fishes.     

Mangroves Enhance Reef Fish Abundance at the Caribbean Regional Scale

Several studies conducted at the scale of islands, or small sections of continental coastlines, have suggested that mangrove habitats serve to enhance fish abundances on coral reefs, mainly by providing nursery grounds for several ontogenetically-migrating species. However, evidence of such enhancement at a regional scale has not been reported, and recently, some researchers have questioned the mangrove-reef subsidy effect. In the present study, using two different regression approaches, we pursued two questions related to mangrove-reef connectivity at the Caribbean regional scale: (1) Are reef fish abundances limited by mangrove forest area?; and (2) Are mean reef fish abundances proportional to mangrove forest area after taking human population density and latitude into account? Specifically, we tested for Caribbean-wide mangrove forest area effects on the abundances of 12 reef fishes that have been previously characterized as “mangrove-dependent”. Analyzed were data from an ongoing, long-term (20-year) citizen-scientist fish monitoring program; coastal human population censuses; and several wetland forest information sources. Quantile regression results supported the notion that mangrove forest area limits the abundance of eight of the 12 fishes examined. Linear mixed-effects regression results, which considered potential human (fishing and habitat degradation) and latitudinal influences, suggested that average reef fish densities of at least six of the 12 focal fishes were directly proportional to mangrove forest area. Recent work questioning the mangrove-reef fish subsidy effect likely reflects a failure to: (1) focus analyses on species that use mangroves as nurseries, (2) consider more than the mean fish abundance response to mangrove forest extent; and/or (3) quantitatively account for potentially confounding human impacts, such as fishing pressure and habitat degradation. Our study is the first to demonstrate at a large regional scale (i.e., the Wider Caribbean) that greater mangrove forest size generally functions to increase the densities on neighboring reefs of those fishes that use these shallow, vegetated habitats as nurseries.     

Autumn use of woody snags by fishes in backwater and channel border habitats of a large river

Snags are important to fish communities in small rivers and streams, but their importance to fishes in large rivers has not been investigated. This study examined snag use by fishes during autumn in backwater and channel border habitats in the upper Mississippi River, and compared these to fish communities in reference sites without snags. Species assemblages differed significantly between backwater and channel border habitats, and between snag and reference sites within the channel border, likely responding to differences in substrate, depth, and current velocity. In both habitats, average fish biomass and abundance were higher (2 to 50 ×) at snag sites than at reference sites, but these differences were significant only for channel border biomass. Fish taxa richness differed between backwater and channel border habitats, but not between snag and reference sites. Most large piscivorous fishes (e.g., Micropterus spp., Stizostedion spp.), several insectivorous fishes (Lepomis macrochirus, Ambloplites rupestris, Minytrema melanops), and a few prey fishes (L. macrochirus, Notropis atherinoides) were significantly more abundant at snag sites than at reference sites, suggesting active selection of snags for foraging or protection. Snag quality, as assessed by a snag rating index, had a direct effect on attracting fish communities with greater biomass, especially within the channel border habitat. These results indicate that snags are important habitat for fish communities in both backwaters and channel border habitats of the upper Mississippi River.     

Artificial Spawning Habitats Improve Egg Production of a Declining Diadromous Fish,Galaxias maculatus (Jenyns, 1842)

Anthropogenic impacts from urbanization, deforestation, and agriculture have degraded the riparian margins of waterways worldwide. In New Zealand, such impacts have caused changes in native vegetation, enhanced invasion by exotic grasses, and altered river bank morphology. One consequence has been a great reduction in obligate spawning habitat of a diadromous fish, Galaxias maculatus. Juvenile G. maculatus comprise a culturally important fishery that has been considerably reduced over recent decades. Rehabilitation of riparian vegetation needed for spawning is relatively straightforward, but slow. We hypothesized that artificial spawning habitats could accelerate restoration of fish egg production by creating an environment that would support at least the same density and survival of eggs as non‐impacted vegetation. We tested three artificial devices (straw bales, straw tubes, and moss tubes) in degraded and intact sites. Eggs were laid in all of these with numbers and survival usually exceeding that in riparian grasses. Where habitat was degraded, artificial spawning habitats yielded up to 10,000 eggs compared to none in nearby natural spawning habitat. The ground‐level environment of artificial habitat was similar to that of intact vegetation in buffering ambient temperature and humidity fluctuations. Crucial properties of the artificial habitats were (1) shelter to provide shade and hold moisture; (2) accessibility to allow adult fish to deposit and fertilize eggs; and (3) robustness to provide reliable surfaces and protection for the eggs during their development. We show that artificial spawning habitats are a viable short‐term alternative to rehabilitating spawning habitat while legacy effects abate and riparian vegetation recovers.     

The future distribution of river fish: The complex interplay of climate and land use changes,species dispersal and movement barriers

The future distribution of river fishes will be jointly affected by climate and land use changes forcing species to move in space. However, little is known whether fish species will be able to keep pace with predicted climate and land use‐driven habitat shifts, in particular in fragmented river networks. In this study, we coupled species distribution models (stepwise boosted regression trees) of 17 fish species with species‐specific models of their dispersal (fish dispersal model FIDIMO) in the European River Elbe catchment. We quantified (i) the extent and direction (up‐ vs. downstream) of predicted habitat shifts under coupled “moderate” and “severe” climate and land use change scenarios for 2050, and (ii) the dispersal abilities of fishes to track predicted habitat shifts while explicitly considering movement barriers (e.g., weirs, dams). Our results revealed median net losses of suitable habitats of 24 and 94 river kilometers per species for the moderate and severe future scenarios, respectively. Predicted habitat gains and losses and the direction of habitat shifts were highly variable among species. Habitat gains were negatively related to fish body size, i.e., suitable habitats were projected to expand for smaller‐bodied fishes and to contract for larger‐bodied fishes. Moreover, habitats of lowland fish species were predicted to shift downstream, whereas those of headwater species showed upstream shifts. The dispersal model indicated that suitable habitats are likely to shift faster than species might disperse. In particular, smaller‐bodied fish (<200 mm) seem most vulnerable and least able to track future environmental change as their habitat shifted most and they are typically weaker dispersers. Furthermore, fishes and particularly larger‐bodied species might substantially be restricted by movement barriers to respond to predicted climate and land use changes, while smaller‐bodied species are rather restricted by their specific dispersal ability.     

Differential growth in estuarine and freshwater habitats indicated by plasma IGF1 concentrations and otolith chemistry in Dolly Varden Salvelinus malma

This study employed a combination of otolith microchemistry to indicate the recent habitat use, and plasma concentrations of the hormone insulin‐like growth factor 1 (IGF1) as an index of recent growth rate, to demonstrate differences in growth and habitat use by Dolly Varden Salvelinus malma occupying both freshwater and estuarine habitats in south‐west Alaska. Extensive sampling in all habitats revealed that fish had higher IGF1 levels in estuarine compared to lake habitats throughout the summer, and that the growth rates in different habitats within the estuary varied seasonally. In addition, otolith microchemistry indicated differentiation in estuarine habitat use among individual S. malma throughout summer months. Although growth in the estuary was higher than in fresh water in nearly all sites and months, the benefits and use of the estuarine habitats varied on finer spatial scales. Therefore, this study further illustrates the diverse life histories of S. malma and indicates an evaluation of the benefits of marine waters needs to include sub‐estuary scale habitat use.     

Changes in rocky reef fish assemblages throughout an estuary with a restricted inlet

Rocky reef habitat is common in many estuaries, yet its role as a habitat for fishes is poorly understood. There is also limited understanding of how access of coastal species into estuaries and habitat quality can affect the distribution of rocky reef fishes within estuaries. This study used baited remote underwater video stations to determine spatial patterns in fish assemblages associated with rocky reef habitat throughout a barrier estuary with a permanently open but restricted inlet. Estuarine rocky reefs provided habitat for a diverse assemblage of fishes, many of which were large juveniles and subadults. In the absence of a pronounced salinity or temperature gradient, a clear transition in fish assemblages occurred from coastal waters, through the inlet channel, to the central estuary, and into the inner estuary. The inlet channel, notably its narrowness and length, limits tidal input into this estuary, which acts as a significant impediment to the dispersal of many coastal fishes, and insufficient habitat excludes many coastal rocky reef species from the inner estuary. This study highlights the need to recognise estuarine rocky reefs as providing habitat for diverse fish assemblages and the role inlets play in restricting access of coastal species.     

Comparative use of side and main channels by small‐bodied fish in a large,unimpounded river

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Habitat choice and recruitment of tropical fishes on temperate coasts of Japan

Tropical reef corals are expanding on Japanese temperate coasts in response to rising sea surface temperatures, and many tropical fish juveniles have been observed routinely in these coral habitats. The present study explored how offshore tropical fish larvae locate coral habitat on the temperate coasts of Japan. Settlement-stage larvae were sampled between July and October 2009–2011 with light traps anchored on coral-replete and coral-free habitats (rocky habitats) at two-level distance (distance between each habitat type was 6 km and 500 m, respectively). Larval abundance was significantly higher on the coral-dominated habitat than that on the rocky habitat at both short and long distance sites, suggesting that coral habitats attract offshore tropical fish larvae. In underwater visual survey, Chaetodontidae and Pomacentridae juveniles were more abundant in coral habitats than in rocky habitats at both the sites, and a laboratory habitat choice experiment demonstrated that these larvae showed a preference for corals rather than rocks. In contrast, densities of juvenile Mullidae did not differ between the coral and rocky habitats, and the larvae did not show a substrate preference in the habitat choice experiment. These observations suggest that habitat choice at settlement possibly accounts for the differences in settlement patterns of tropical fishes between the two habitats. Taken together, our results showed that most tropical fish larvae colonize their settlement coast at a scale of ~0.5 km, and that they may locate coral habitats after reaching a reef. Moreover, the results suggest that coral habitat expansion on temperate coasts will lead to an increase in coral-associated tropical fishes and will change assemblage structures of fishes on temperate coasts.     

Tradeoffs between fine‐scale site measurements and coarse sensory data for long‐term monitoring of pulsed wetlands

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Reproductive strategies of Amazonian stream fishes and their fine‐scale use of habitat are ordered along a hydrological gradient

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Habitat Use by Fishes in Coral Reefs,Seagrass Beds and Mangrove Habitats in the Philippines

Understanding the interconnectivity of organisms among different habitats is a key requirement for generating effective management plans in coastal ecosystems, particularly when determining component habitat structures in marine protected areas. To elucidate the patterns of habitat use by fishes among coral, seagrass, and mangrove habitats, and between natural and transplanted mangroves, visual censuses were conducted semiannually at two sites in the Philippines during September and March 2010–2012. In total, 265 species and 15,930 individuals were recorded. Species richness and abundance of fishes were significantly higher in coral reefs (234 species, 12,306 individuals) than in seagrass (38 species, 1,198 individuals) and mangrove (47 species, 2,426 individuals) habitats. Similarity tests revealed a highly significant difference among the three habitats. Fishes exhibited two different strategies for habitat use, inhabiting either a single (85.6% of recorded species) or several habitats (14.4%). Some fish that utilized multiple habitats, such as Lutjanus monostigma and Parupeneus barberinus, showed possible ontogenetic habitat shifts from mangroves and/or seagrass habitats to coral reefs. Moreover, over 20% of commercial fish species used multiple habitats, highlighting the importance of including different habitat types within marine protected areas to achieve efficient and effective resource management. Neither species richness nor abundance of fishes significantly differed between natural and transplanted mangroves. In addition, 14 fish species were recorded in a 20-year-old transplanted mangrove area, and over 90% of these species used multiple habitats, further demonstrating the key role of transplanted mangroves as a reef fish habitat in this region.     

Fish habitat association in an Ozark stream

Synopsis Associations of fishes in physically distinct habitats (riffles, inlets and pools) of Flint Creek were studied to evaluate critically the habitat-guild concept — the notion that fishes associate with patches of stream habitat in discrete groups. There was little evidence of significant interspecific association at the habitat level. Most fishes were very generalized in their habitat-use patterns. Faunal similarity between habitats was unrelated to physical-habitat similarity. Assemblages from physically distinct habitats were little different from those from physically similar habitats. The structure of the associations (constancy within groups of commonly occurring species) varied seasonally and from site to site. There were constant associations in pools from summer through fall and this coincided with conditions of high fish density and low food availability, suggesting that the pattern resulted from past or present interaction between species. However, the timing also coincided with recruitment of young. Pools were the favored habitats of young-of-year fishes which dominated assemblages in these areas during summer and fall months. This apparently adaptive pattern of habitat association, operating in tandem with local reproductive success could have been responsible for the constancy observed in pools. Most of the species considered here made use of a variety of habitat conditions over the course of their life histories. Individual patches of habitat satisfied the needs of few fish, and thus, seemed too small a scale for the study of community-assembly mechanisms. There was better evidence of interspecies association at the scale of two or more of these habitat areas combined.     

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.     

Importance of live coral habitat for reef fishes

Live corals are the key habitat forming organisms on coral reefs, contributing to both biological and physical structure. Understanding the importance of corals for reef fishes is, however, restricted to a few key families of fishes, whereas it is likely that a vast number of fish species will be adversely affected by the loss of live corals. This study used data from published literature together with independent field based surveys to quantify the range of reef fish species that use live coral habitats. A total of 320 species from 39 families use live coral habitats, accounting for approximately 8 % of all reef fishes. Many of the fishes reported to use live corals are from the families Pomacentridae (68 spp.) and Gobiidae (44 spp.) and most (66 %) are either planktivores or omnivores. 126 species of fish associate with corals as juveniles, although many of these fishes have no apparent affiliation with coral as adults, suggesting an ontogenetic shift in coral reliance. Collectively, reef fishes have been reported to use at least 93 species of coral, mainly from the genus Acropora and Porities and associate predominantly with branching growth forms. Some fish associate with a single coral species, whilst others can be found on more than 20 different species of coral indicating there is considerable variation in habitat specialisation among coral associated fish species. The large number of fishes that rely on coral highlights that habitat degradation and coral loss will have significant consequences for biodiversity and productivity of reef fish assemblages.     

Analysis of the blennioid assemblages associated with different rocky shore habitats in the Ligurian Sea

The differences among blennioid assemblages (families Blenniidae and Tripterygiidae) on different habitats were assessed at two localities of the Ligurian Sea, namely Arenzano and Riva Trigoso. The assemblage composition and species relative density were evaluated visually on four different habitats of diverse wave exposure and substratum orientation (macro‐habitat characteristics): two vertical intertidal and subtidal habitats (exposed and sheltered rockwalls) and two horizontal subtidal habitats (semi‐exposed flat rock and boulders and pebbles). Each habitat was also characterized in relation to micro‐habitat features, such as substratum complexity, heterogeneity and amount of algae cover. Patterns of differences among habitats in assemblage variables and fish density, and the influences of macro‐ and micro‐habitat features on these patterns were studied at small (within localities) and large (across localities) spatial scales. Higher values of species richness (S), diversity and evenness (J) were generally associated with vertical habitats, as a result of a positive correlation with substratum orientation. The presence of an intertidal zone in the rockwall habitats may partially explain the observed differences in assemblage variables between vertical and horizontal habitats. The strength of relationships between S, and J and the other investigated habitat variables (exposure, complexity, heterogeneity and algae cover) varied greatly depending on spatial scale. All these relationships were positive, except for complexity. Significant variation in the assemblage total density among habitats was recorded only at Arenzano, where a larger number of fishes were counted on rockwalls rather than on the horizontal habitats. The positive effect of orientation on fish total density was strictly dependent on spatial scale. Fish total density showed a negative correlation with complexity and a positive correlation with heterogeneity, both relationships being unaffected by spatial scale. The unexpected relationship with complexity was probably due to the fact that, in the most complex habitat (i.e. boulder and pebbles), the potential positive effect of high complexity on fish density might be overcome by the negative influence of other environmental features, such as horizontal orientation and low wave exposure. Complexity and heterogeneity thus seemed good predictors of fish total density, but their role needs to be carefully interpreted. The most marked differences in species composition and relative density were found between rockwalls and the other habitats, mostly due to an unbalanced distribution of some stenoecious species. Variations in species relative density were related to different combinations of both macro‐ and micro‐habitat features, and these relationships usually changed depending on spatial scale.     

Microhabitat selectivity underpins regional indicators of fish abundance and replenishment

Species with specialized resource use can display strong spatial heterogeneity in abundance according to the availability of their preferred habitats. If these preferences shift with ontogeny, then a wide range of habitats may need to be protected in order to support both adult populations and their replenishment. We explored whether microhabitat selectivity interacts with habitat availability to provide an effective suite of indicators for regional fish abundance and replenishment, using offshore rocky reefs in south-eastern Australia as a case study. We examined generalized additive mixed models (GAMMs) in a full subsets approach to infer the best predictors for adult and juvenile fish density in four diverse families (Labridae, Odacidae, Pomacentridae, Serranidae), based on rapid underwater visual surveys across transects (⿼500 m²), wave exposures (0.3⿿1 km), and sites (0.3⿿48 km). We then examined whether these regional fish-habitat models aligned with the microhabitat electivity of individuals (at scale of <1 m²). Microhabitat selection by reef fishes at the local scale underpinned the most effective habitat indicators for regional heterogeneity in fish abundance, and pointed to critical nursery habitats that support hotspots of juvenile recruitment. Strong species-habitat relationships, such as these, can be combined with broad-scale habitat mapping to assess the potential carrying capacity of focal areas, spatial management zone placements, and nursery habitats that warrant special protection. A number of emerging threats to these key habitat types indicates an urgent need for habitat-based protection and monitoring as a key part of holistic marine ecosystem conservation and management.