Deep Habitats Research Articles

Fishes from the deep demersal habitats off Manado, North Sulawesi, Indonesia and Negros Island, Philippines

This paper is a study of some rare and poorly known deep demersal fishes in two Indo-Pacific localities, one in the central Philippines (off Negros Island) and another off Manado, northern Sulawesi. The occurrence of the shark Indonesian Wobbegong Orectolobus leptolineatus in the Philippines is also confirmed. The recent information on the Indonesian Coelacanth (Latimeria menadoensis) and other fish species are also presented. The presence of an angled-rough shark, which is tentatively identified herein as Oxynotus cf japonicus, is also reported for the first time to occur in North Sulawesi waters, Indonesia. Keywords : Indonesia, Philippines, deep, demersal fishes, habitat.

Deep sea habitats in the chemical warfare dumping areas of the Baltic Sea

The Baltic Sea is a severely disturbed marine ecosystem that has previously been used as a dumping ground for Chemical Warfare Agents (CW). The presence of unexploded underwater ordnance is an additional risk factor for offshore activities and an environmental risk for the natural resources of the sea. In this paper, the focus is on descriptions of the marine habitat based on the observations arising from studies linked to the CHEMSEA, MODUM and DAIMON projects. Investigated areas of Bornholm, Gotland and Gdańsk Deeps are similarly affected by the Baltic Sea eutrophication, however, at depths greater than 70m several differences in local hydrological regimes and pore-water heavy metal concentrations between those basins were observed. During the lifespan of presented studies, we were able to observe the effects of Major Baltic Inflow, that started in December 2014, on local biota and their habitats, especially in the Bornholm Deep area. Reappearance of several meiofauna taxa and one macrofauna specimen was observed approximately one year after this phenomenon, however it's ecological effects already disappeared in March 2017. According to our findings and to the EUNIS Habitat Classification, the three reviewed areas should be characterized as Deep Sea Muddy Sands, while the presence of suspicious bomb-like objects both beneath and on top of the sediments confirms their CW dumpsite status.

Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds

The past decade of scientific ocean drilling has revealed seemingly ubiquitous, slow-growing microbial life within a range of deep biosphere habitats. Integrated Ocean Drilling Program Expedition 337 expanded these studies by successfully coring Miocene-aged coal beds 2 km below the seafloor hypothesized to be "hot spots" for microbial life. To characterize the activity of coal-associated microorganisms from this site, a series of stable isotope probing (SIP) experiments were conducted using intact pieces of coal and overlying shale incubated at in situ temperatures (45 °C). The 30-month SIP incubations were amended with deuterated water as a passive tracer for growth and different combinations of 13C- or 15N-labeled methanol, methylamine, and ammonium added at low (micromolar) concentrations to investigate methylotrophy in the deep subseafloor biosphere. Although the cell densities were low (50-2,000 cells per cubic centimeter), bulk geochemical measurements and single-cell-targeted nanometer-scale secondary ion mass spectrometry demonstrated active metabolism of methylated substrates by the thermally adapted microbial assemblage, with differing substrate utilization profiles between coal and shale incubations. The conversion of labeled methylamine and methanol was predominantly through heterotrophic processes, with only minor stimulation of methanogenesis. These findings were consistent with in situ and incubation 16S rRNA gene surveys. Microbial growth estimates in the incubations ranged from several months to over 100 y, representing some of the slowest direct measurements of environmental microbial biosynthesis rates. Collectively, these data highlight a small, but viable, deep coal bed biosphere characterized by extremely slow-growing heterotrophs that can utilize a diverse range of carbon and nitrogen substrates.

A major range extension for Carcharhinus altimus (Springer, 1950) in the South Pacific Ocean

The occurrence of the bignose shark Carcharhinus altimus at Ducie Island, Pitcairn Islands is reported for the first time based upon re-identification of four museum voucher specimens. The presence of a pregnant female and a juvenile confirms C. altimus breeds at Ducie Island and should be considered resident there. The specimens had been misidentified as the grey reef shark, C. amblyrhynchos, emphasising the ongoing value of collecting museum voucher specimens of supposedly common species. The occurrence of C. altimus at Ducie Island suggests resident populations of C. altimus are likely to occur throughout the tropical and subtropical Pacific Ocean but may have been overlooked due to their preference for deep demersal habitats during the day, or misidentification as other Carcharhinus species.

Human Assisted Robotic Vehicle Studies - A conceptual end-to-end mission architecture

With current space exploration roadmaps indicating the Moon as a proving ground on the way to human exploration of Mars, it is clear that human-robotic partnerships will play a key role for successful future human space missions. This paper details a conceptual end-to-end architecture for an exploration mission in cis-lunar space with a focus on human-robot interactions, called Human Assisted Robotic Vehicle Studies (HARVeSt). HARVeSt will build on knowledge of plant growth in space gained from experiments on-board the ISS and test the first growth of plants on the Moon. A planned deep space habitat will be utilised as the base of operations for human-robotic elements of the mission. The mission will serve as a technology demonstrator not only for autonomous tele-operations in cis-lunar space but also for key enabling technologies for future human surface missions. The successful approach of the ISS will be built on in this mission with international cooperation. Mission assets such as a modular rover will allow for an extendable mission and to scout and prepare the area for the start of an international Moon Village.

Modelling the future spread of native and alien congeneric species in subterranean habitats — the case of Meta cave-dwelling spiders in Great Britain

The threshold zones between the epigean and hypogean environments are generally characterized by less harsh ecological conditions than deep subterranean habitats, and usually support a greater abundance of organisms. Transitional habitats such as these should be more easily colonised by alien species, especially by those possessing exaptations suitable for subterranean life. In spite of this, few studies have been conducted to unravel the ecological dynamics between native and alien species in the habitats situated at the epigean/hypogean interface. A unique test case is offered by cave-dwelling Meta orb-weaver spiders in Great Britain (Araneae: Tetragnathidae). One species, M. menardi, is a widespread native, whilst M. bourneti is believed to be a recently introduced (1940s) species, that has since become established in the south-eastern part of the country. Species distribution models (SDM) were used to predict current and future habitat suitability for the two species, generating hypotheses regarding their distribution in different global warming scenarios. Model projections indicate that the two species respond to similar environmental variables. Seasonal temperature variations at the surface and elevation are the main factors explaining the distribution of both species, whereas annual precipitation, daily temperature range and limestone distribution contributed little to the model performance. It is predicted that due to climate change, there will be poleward shifts in the ranges of both species. However, the native species M. menardi will primarily be able to exploit suitable areas which will appear northward to their current distribution, and M. bourneti will colonise empty niches left available by its congeneric. The analytical framework employed in this paper may be easily adapted to other subterranean systems and species, stimulating future studies focusing on the distribution of native and alien species in extreme environments.

Major phylum-level differences between porefluid and host rock bacterial communities in the terrestrial deep subsurface.

Earth's deep subsurface biosphere (DSB) is home to a vast number and wide variety of microorganisms. Although difficult to access and sample, deep subsurface environments have been probed through drilling programs, exploration of mines and sampling of deeply sourced vents and springs. In an effort to understand the ecology of deep terrestrial habitats, we examined bacterial diversity in the Sanford Underground Research Facility (SURF), the former Homestake gold mine, in South Dakota, USA. Whole genomic DNA was extracted from deeply circulating groundwater and corresponding host rock (at a depth of 1.45 km below ground surface). Pyrotag DNA sequencing of the 16S rRNA gene revealed diverse communities of putative chemolithoautotrophs, aerobic and anaerobic heterotrophs, numerous candidate phyla and unique rock-associated microbial assemblage. There was a clear and near-total separation of communities between SURF deeply circulating fracture fluids and SURF host-rocks. Sequencing data from SURF compared against five similarly sequenced terrestrial subsurface sites in Europe and North America revealed classes Clostridia and Betaproteobacteria were dominant in terrestrial fluids. This study presents a unique analysis showing differences in terrestrial subsurface microbial communities between fracture fluids and host rock through which those fluids permeate.

Habitat Associations of Juvenile Burbot in a Tributary of the Kootenai River

AbstractBurbot Lota lota in the lower Kootenai River, Idaho, have been the focus of extensive conservation efforts, particularly conservation aquaculture. One of the primary management strategies has been the release of Burbot into small tributaries in the Kootenai River basin, such as Deep Creek. Since 2012, approximately 12,000 juvenile Burbot have been stocked into Deep Creek; however, little is known about the habitat use of stocked Burbot. The objective of this study was to evaluate habitat associations of juvenile Burbot in Deep Creek. Fish and habitat were sampled from 58 reaches of the creek. Regression models suggested that Burbot moved little after stocking and were associated with areas of high mean depth and coarse substrate. This study provides additional knowledge on habitat associations of juvenile Burbot and suggests that managers should consider selecting deep habitats with coarse substrate for stocking locations.Received December 15, 2016; accepted May 22, 2017 Published online July 31, 2017

Habitat associations and distribution of the hyperbenthic shrimp, Nauticaris marionis, around the sub-Antarctic Prince Edward Islands

The association of organisms with particular habitats and habitat-forming organisms, can strongly influence species distributions, interactions and wider ecosystem services. At the sub-Antarctic Prince Edward Islands, the caridean shrimp Nauticaris marionis is a principal part of the benthic ecosystem, occurring between ca. 50m and 600m. Its role as a trophic link between the primary productivity and higher predators is established, but little is understood of its in situ habitat usage and associations or of how these structure patterns of abundance. We investigated these aspects directly using a benthic camera sled, sampling 27 stations between 50m and 500m. Substratum type was characterised, and estimates of percentage cover of the 13 main groups of habitat-forming epibenthic taxa were made, alongside absolute counts of N. marionis within ‘digital quadrats’ drawn from 300m transects. The distribution of N. marionis was influenced by depth, substratum type and overall biogenic cover, being limited to habitats between 50 and 160m depth on mud or gravel substrata only, and having > 50% biogenic cover. The presence/absence of N. marionis related to significantly different epibenthic assemblages (termed biogenic habitats), but this effect was contingent on depth. Likewise, densities of N. marionis were significantly affected by biogenic habitat type, identifying an association with two biogenic habitat groups, one dominated by red-algae, the other by structurally complex bryozoan species. These associations likely relate to the structural complexity of the two habitat groups, rather than the specific taxa involved. The apparent absence of N. marionis at depths > 160m contrasts with earlier records and poses questions about the trophic importance of the shrimp in deeper habitats.

Food web properties of the recently constructed, deep subtropical Fei-Tsui Reservoir in comparison with the ancient Lake Biwa

Using carbon and nitrogen stable isotope analysis, we characterised food web properties of the deep subtropical Fei-Tsui Reservoir (FTR), which was recently altered from a lotic to a lentic system after dam construction. In the littoral zone, zoobenthos showed strong reliance (83.9%) on benthic algal production. Zoobenthos were never found in the profundal zone because of anoxia. Zooplankton depleted 13C more than that of particulate organic matter as their putative food source, suggesting a contribution of methane-derived carbon to pelagic food webs. Excluding juveniles, non-native and fluvial species, adult fish showed strong reliance (on average 80.9%) on benthic production, weakly coupled with pelagic food webs. These results contrast low benthic production reliance (on average 27.4%) for a fish community in Lake Biwa, which is also classified as a subtropical lake. Both lakes are characterised by deep pelagic waters but quite different in their geological ages, suggesting that the aquatic communities in the FTR have fluvial origins, and their lacustrine history was too short for them to adapt to newly emerged deep pelagic habitat. Our isotope data are useful as a reference of newly established lentic food webs to monitor ongoing ecological and evolutionary dynamics as a result of anthropogenic disturbances.

Assessment of the impact of salvaging the Costa Concordia wreck on the deep coralligenous habitats

The coralligenous habitats found in the Mediterranean Sea are hotspots comparable in biodiversity to tropical reefs. Coralligenous reefs are vulnerable to many human pressures, thus they are among the most threatened habitats in the Mediterranean Sea. In this study, we assessed the impacts on coralligenous habitats of activities associated with salvaging the wreck of the Costa Concordia cruise ship. After its partial foundering in 2012, the Costa Concordia remained adjacent to the eastern coast of Giglio Island (Tuscany, Italy), in the Tyrrhenian Sea, for over two years. Its salvage required high-impact engineering works, during the course of which monitoring of benthic communities was undertaken. We performed Rapid Visual Assessment (RVA) sampling (using recorded video) from 17 stations located between 35 and 76m depth and characterized by coralligenous habitats. Sampling activity was performed during the summers of 2012, 2013, and 2014. In parallel, chemical and physical water parameters were measured continuously from summer 2012 to the end of summer 2014, in order to detect any perturbation in natural conditions caused by salvage activities. We assessed the ecological quality of coralligenous habitats by applying the COARSE (COralligenous Assessment by ReefScape Estimate) index, based on the RVA approach. Slight modifications were applied to one of the descriptors of the COARSE index in order to adjust for study site features. There was clear evidence of a reduction in coralligenous habitats quality. Assemblages, slope, type of pressure, and distance from the source of disturbance played a pivotal role in characterizing bottom quality. The index was shown to have an easy and cost-effective application, even in waters deeper than its calibration specification; furthermore, the modification reported here may increase its potential applications.

Fauna and habitat types driven by turbidity currents in the lobe complex of the Congo deep-sea fan

This study characterizes the habitats and megafaunal community of the Congo distal lobe complex driven by turbidity currents through the use of remotely operated vehicle (ROV) still imagery transects covering distances in the order of kilometers. In this sedimentary, abyssal area about 5000m deep and 750km offshore from western Africa, large quantities of deposited organic material supplied by the Congo River canyon and channel support aggregations of large sized foraminifers (Bathysiphon sp.) and vesicomyid clams (Christineconcha regab, Abyssogena southwardae) often associated with methane cold seeps, as well as opportunistic deep-sea scavengers. Additionally, bacterial mats, assumed to be formed by large sulfur-oxidizing filamentous bacteria (Beggiatoa type), and black patches of presumably reduced sediment were seen which are, together with sulfur-oxidizing symbiont- bearing vesicomyids, indicators of sulfide-rich sediments. Habitat and faunal distribution were analyzed in relation to the microtopography obtained with the ROV multibeam echosounder, at three sites from the entrance of the lobe complex where the channel is still deep, to the main, flatter area of turbidite deposition. Specific characteristics of the system influence animal distributions: both the forams and the vesicomyid clams tended to avoid the channels characterized by high-speed currents, and are therefore preferentially located along channel flanks affected by sliding, and on levees formed by channel overspill. Foram fields are found in flat areas and form large fields, whereas the vesicomyids have a patchy distribution and appear to show a preference for regions of local topographical relief such as slide scars or collapsed blocks of sediments, which likely facilitate sulfide exhumation. The colonization of sulfide rich sediments by vesicomyids is limited, but nonetheless was seen to occur in the main deposition area where they have to cope with very high sedimentation rates (up to 20cm/yr) and frequent turbidity currents. Other biological adaptations to the local conditions likely determine the presence and survival of animals in the system: large agglutinated forams are known to be adept at quickly colonizing disturbed sediment and capitalizing on abundant but irregular food sources, and vesicomyid clams have a mobile lifestyle that enables them to maintain their population in the ever changing landscape of sulfide-rich sediment outcrops. Turbiditic systems appear to be intermediate between other energy rich habitats sustaining chemosynthesis in the deep sea, being locally less stable in terms of energy supply than cold seeps, limiting the number of cold-seep specialists able to colonize, but constituting a longer lived habitat than food falls. Turbidite fans therefore represent distinct deep sea habitats that contribute to sustaining populations of both chemosynthesis-based and opportunistic taxa in the deep-sea.

Global climate change and regional biotic responses: two hydrozoan tales

ABSTRACTGlobal climate change is affecting the planet’s biodiversity, altering marine ecosystems and modifying species distributions. Using historical and recently collected data, changes in depth distribution of two hydrozoan taxa (Ectopleura crocea and Millepora spp.) with different life histories, ecology and geographic distributions were compared to trends in sea surface temperature (SST). Ectopleura crocea, a temperate species, used to be very common in Italian seas on shallow water artificial substrata, where it settled mainly between spring and autumn. In the Maldives, three species of the tropical hydrocoral Millepora (M. platyphylla, M. latifolia and M. tenera) were reported as common from the early 20th century until recently. Millepora underwent mass mortality during a bleaching event linked to a thermal positive anomaly caused by El Niño and lasting from April to July, 1998. Similarly, E. crocea disappeared from Italian surface waters where it was once abundant. Both the temperate and the tropical hydrozoans survived at moderate depth and recolonized shallow water habitats in recent years. These two hydrozoan examples support the depth refugia hypothesis, according to which marine organisms may shift to deeper habitats to avoid shallow water heatwaves and increased temperature variability. Return to shallow water has been possible only after acclimation such as shifting season of occurrence from summer to winter–spring (E. crocea in Italian seas) or possibly through species replacement (Millepora in the Maldives). Continued field research is needed to understand and evaluate the effect of climate change on marine species distribution.

Habitat preference of Viminella flagellum (Alcyonacea: Ellisellidae) in relation to bathymetric variables in southeastern Sardinian waters

The whip-like gorgonian Viminella flagellum (Alcyonacea, Ellisellidae) has an Atlantic-Mediterranean distribution. In Italian seas, the species is a common component of deep-sea rocky environments from the north-western Mediterranean area to the Strait of Sicily.V. flagellum grows in deep habitats, sometimes outlining the environment with dense forests. This work describes its habitat in an area in the southeastern Sardinian waters (central-western Mediterranean Sea), where a dense forest of the species was found. The specimens were filmed and photographed between 120 and 260m depth with a Remotely Operated Vehicle (ROV).High-resolution multibeam echosounder (MBES) bathymetry data of the area were acquired and morphometric parameters were derived. These parameters were assumed to be relevant for the distribution of the whip-like gorgonians and were used in an Ecological Niche Factor Analysis (ENFA) to explore the niche and habitat preference of the target species. In order to identify which Eco-geographical variables are useful to predict coral distribution, we used the Maximum Entropy model (MaxEnt). Our results gave a first description of the habitat preference of V. flagellum. Specimens were found in a distinctive habitat, with respect to the overall features of the entire studied area which was characterised by a marked slope in a simple rocky seabed system, within a water depth range of 125–150m.

Can deep reefs rescue shallow ones?

Scientists test the idea that species squeezed out of shallow coral reefs may find a refuge in deeper habitats.

Into the Twilight Zone.

Naturalist Rich Pyle plumbs the undiscovered realm of deep, dimly lit reefs.

Squamation and ecology of thelodonts.

Thelodonts are an enigmatic group of Paleozoic jawless vertebrates that have been well studied from taxonomical, biostratigraphic and paleogeographic points of view, although our knowledge of their ecology and mode of life is still scant. Their bodies were covered by micrometric scales whose morphology, histology and the developmental process are extremely similar to those of extant sharks. Based on these similarities and on the well-recognized relationship between squamation and ecology in sharks, here we explore the ecological diversity and lifestyles of thelodonts. For this we use classic morphometrics and discriminant analysis to characterize the squamation patterns of a significant number of extant shark species whose ecology is well known. Multivariate analyses have defined a characteristic squamation pattern for each ecological group, thus establishing a comparative framework for inferring lifestyles in thelodonts. We then use this information to study the squamation of the currently described 147 species of thelodonts, known from both articulated and disarticulated remains. Discriminant analysis has allowed recognizing squamation patterns comparable to those of sharks and links them to specific ecological groups. Our results suggest a remarkable ecological diversity in thelodonts. A large number of them were probably demersal species inhabiting hard substrates, within caves and crevices in rocky environments or reefs, taking advantage of the flexibility provided by their micromeric squamations. Contrary to classical interpretations, only few thelodonts were placed among demersal species inhabiting sandy and muddy substrates. Schooling species with defensive scales against ectoparasites could be also abundant suggesting that social interactions and pressure of ectoparasites were present in vertebrates as early the Silurian. The presence of species showing scales suggestive of low to moderate speed and a lifestyle presumably associated with open water environments indicates adaptation of thelodonts to deep water habitats. Scale morphology suggests that some other thelodonts were strong-swimming pelagic species, most of them radiating during the Early Devonian in association with the Nekton Revolution.

The Geomycology of Elemental Cycling and Transformations in the Environment.

Geomicrobiology addresses the roles of microorganisms in geological and geochemical processes, and geomycology is a part of this topic focusing on the fungi. Geoactive roles of fungi include organic and inorganic transformations important in nutrient and element cycling, rock and mineral bioweathering, mycogenic biomineral formation, and metal-fungal interactions. Lichens and mycorrhizas are significant geoactive agents. Organic matter decomposition is important for cycling of major biomass-associated elements, e.g., C, H, N, O, P, and S, as well as all other elements found in lower concentrations. Transformations of metals and minerals are central to geomicrobiology, and fungi affect changes in metal speciation, as well as mediate mineral formation or dissolution. Such mechanisms are components of biogeochemical cycles for metals as well as associated elements in biomass, soil, rocks, and minerals, e.g., S, P, and metalloids. Fungi may have the greatest geochemical influence within the terrestrial environment. However, they are also important in the aquatic environment and are significant components of the deep subsurface, extreme environments, and habitats polluted by xenobiotics, metals, and radionuclides. Applications of geomycology include metal and radionuclide bioleaching, biorecovery, detoxification, bioremediation, and the production of biominerals or metal(loid) elements with catalytic or other properties. Adverse effects include biodeterioration of natural and synthetic materials, rock and mineral-based building materials (e.g., concrete), cultural heritage, metals, alloys, and related substances and adverse effects on radionuclide mobility and containment. The ubiquity and importance of fungi in the biosphere underline the importance of geomycology as a conceptual framework encompassing the environmental activities of fungi.

Evolution of Anabaenopeptin Peptide Structural Variability in the Cyanobacterium Planktothrix.

Cyanobacteria are frequently involved in the formation of harmful algal blooms wherein, apart from the toxic microcystins, other groups of bioactive peptides are abundant as well, such as anabaenopeptins (APs). The APs are synthesized nonribosomally as cyclic hexapeptides with various amino acids at the exocyclic position. We investigated the presence and recombination of the AP synthesis gene cluster (apnA-E) through comparing 125 strains of the bloom-forming cyanobacterium Planktothrix spp., which were isolated from numerous shallow and deep water habitats in the temperate and tropical climatic zone. Ten ecologically divergent strains were purified and genome sequenced to compare their entire apnA-E gene cluster. In order to quantify apn gene distribution patterns, all the strains were investigated by PCR amplification of 2 kbp portions of the entire apn gene cluster without interruption. Within the 11 strains assigned to P. pseudagardhii, P. mougeotii, or P. tepida (Lineage 3), neither apnA-E genes nor remnants were observed. Within the P. agardhii/P. rubescens strains from shallow waters (Lineage 1, 52 strains), strains both carrying and lacking apn genes occurred, while among the strains lacking the apnA-E genes, the presence of the 5′end flanking region indicated a gene cluster deletion. Among the strains of the more derived deep water ecotype (Lineage 2, 62 strains), apnA-E genes were always present. A high similarity of apn genes of the genus Planktothrix when compared with strains of the genus Microcystis suggested its horizontal gene transfer during the speciation of P. agardhii/P. rubescens. Genetic analysis of the first (A1-) domain of the apnA gene, encoding synthesis of the exocyclic position of the AP molecule, revealed four genotype groups that corresponded with substrate activation. Groups of genotypes were either related to Arginine only, the coproduction of Arginine and Tyrosine or Arginine and Lysine, or even the coproduction of Arginine, Tyrosine, and Lysine in the exocyclic position of the AP-molecule. The increased structural diversity resulted from the evolution of apnA A1 genotypes through a small number of positively selected point mutations that occurred repeatedly and independently from phylogenetic association.

Defining critical habitat conditions for the conservation of three endemic and endangered cyprinids in a Mediterranean intermittent river before the onset of drought

Abstract Identifying key factors in species' habitat requirements can be of use in defining critical habitats for their conservation, as well as in assisting the prioritization of habitat restoration actions. So far, most studies on habitat use by freshwater fishes have been focused on widespread and economically important species (e.g. salmonids). This study aimed to identify the early summer habitat use (i.e. before the start of the drought period) of three endemic and endangered Greek cyprinids – the Evrotas chub Squalius keadicus, the Spartian minnowroach Tropidophoxinellus spartiaticus and the Evrotas minnow Pelasgus laconicus, with regard to depth, water velocity, substrate and macrophyte cover. In the case of the chub, habitat use by juvenile and adult fish was assessed separately. Data were collected for each fish group from four habitat types (riffles, runs, glides, pools) by using a modified point‐abundance sampling with an electrofishing device. In total, 120 sampling points were sampled, in two near‐reference perennial reaches of the Evrotas River (southern Greece) in early summer 2014, when there was continuous flow and full connectivity between habitats. All three target species had their highest densities in deeper habitats with low water velocities and depositional substrates such as pools and runs. A high overlap in habitat use was evident for the three species. Habitat use curves based on microhabitat data were created for all species. Μinnowroaches, minnows and large chubs actively selected deep habitats. Minnowroaches and minnows favoured slow‐flowing, vegetated habitats with fine substrate located close to the river bank, while chubs had no clear affinity for particular velocities or substrate types. However, size class comparisons in chub indicated differences in both water depth and velocity. Overall, the results of this study provide the first detailed report of the habitat use of these endangered fish species. These patterns of habitat use highlight the importance of deep habitats that must be preserved as refugia while the drought events progress.