Coastal Ponds Research Articles

Characterizing Juvenile Common Snook and Tarpon Habitat to Guide Conservation and Restoration of Coastal Wetlands

To conserve or restore juvenile fish habitat, resource managers, restoration practitioners, and engineers need fine-scale information to understand what conditions they need to preserve or what specifications are needed to create new habitat. The objective of this study was to develop statistical models using a dataset of 18 coastal ponds in Southwest Florida, USA, to predict the abundance of juvenile common snook Centropomus undecimalis (hereafter snook) and presence of juvenile tarpon Megalops atlanticus, both of which are flagship species used for conservation and restoration of subtropical and tropical wetlands. Model predictors included water conditions and characteristics of vegetation, sediment, and geographic position. Modeling results indicated that juvenile snook used coastal ponds that were directly connected to tidal creeks. In contrast, juvenile tarpon were more likely to be present in coastal ponds that were separated from tidal creeks by dense mangrove forest (e.g., elevation > 0.48 m above Mean Low Water) characterized by highly organic sediment and low dissolved oxygen, to which tarpon are well adapted. Overlap between snook abundance and tarpon presence was greatest where connections between ponds and the nearest tidal creek were at a relatively low elevation (e.g., -0.12 m relative to Mean Low Water). Although these findings are most applicable to management and conservation of populations in areas along the Gulf coast of Florida (i.e., in areas of similar tidal range and coastal geomorphology), incorporating more detailed habitat surveys to better capture landscape context, geomorphology, and connectivity into fish sampling designs should be broadly applicable to estuarine fish ecology.

Emigration of Juvenile Tarpon Megalops atlanticus from Ephemerally Connected Coastal Ponds

Worldwide, coastal wetlands are threatened by disrupted hydrology, urbanization, and sea-level rise. In southwest Florida, coastal wetlands include tidal creeks and coastal ponds, which are the primary habitats used by juvenile Tarpon, Megalops atlanticus, an important sport fish. Coastal ponds can occur near uplands and are ephemerally connected to the open estuary, creating conditions of variable dissolved oxygen and salinity. Juveniles can tolerate wide-ranging abiotic conditions, but little is known about how they egress from their remote nursery habitats, which often requires them to cross > 1 km of mangrove forest to reach the open estuary. The objective of this study was to (1) compare Tarpon body condition among ponds close to the open estuary versus those ponds farther away on the Cape Haze peninsula of Charlotte Harbor, Florida, and (2) using acoustic telemetry determine what factors contribute to Tarpon emigration from the ponds to open estuarine waters. We tested the hypothesis that distinct groups of Tarpon occur in isolated ponds, leading to variation in fish length and body condition, and that opportunities for emigration from these ponds hinge on high water events. No pond stood out as having Tarpon of low body condition. Factors contributing to increased probabilities of Tarpon emigration were low barometric pressure, high-water level, and Tarpon body length. Tarpon emigrated from ponds near tidal creeks during summer king tides, while tropical cyclone conditions were needed to allow for movement from ponds farther in the landscape. The juvenile Tarpon were later detected at the mouths of large rivers 30 km up-estuary. The characterizations of water levels and event criteria needed for successful Tarpon nurseries should aid in habitat conservation and the creation of Tarpon nursery habitat in restoration designs.

Significant temporal variability leads to estimation bias in greenhouse gas emissions from aquaculture pond systems

Rising demand for aquatic products has expanded aquaculture, significantly elevating greenhouse gas (GHG) emissions from the aquaculture ponds. However, the emission estimation shows huge uncertainty. This study employed a meta-analysis of 1060 datasets of CO2, CH4 and N2O fluxes to examine how temporal variability affects GHG emissions from China's aquaculture ponds and to identify key environmental drivers. The results reveal that China’s aquaculture ponds are significant sources of GHGs to the atmosphere, with fluxes of CO2, CH4, and N2O from coastal pond systems at 5.50, 7.41 mg m² h⁻¹, and 16.72 μg m² h⁻¹ during the farming period, and −8.96, 4.33 mg m² h⁻¹, and 44.98 μg m² h⁻¹ during the non-farming period, respectively. Regarding inland pond systems, the fluxes of CO2, CH4, and N2O were 50.48, 5.19 mg m² h⁻¹, and 36.35 μg m² h⁻¹ during farming period, and 0.90, 1.03 mg m² h⁻¹, and 51.46 μg m² h⁻¹ during non-farming period, respectively. Total GHG annual emissions were 42.17 Tg CO2-eq over a 100-year time scale, predominantly from CH4 at 74.11 %, with CO2 contributing to 9.63 %, and N2O to 6.63 %. Post-cultivation drainage significantly shifts biogeochemical conditions and emission patterns, reducing total GHG emissions. Ignoring the non-farming period leads to overestimated CO2 and CH4 emissions, and underestimated N2O emissions. Our study provides new insights into GHG estimation from aquaculture ponds, highlighting the importance of considering temporal variability in GHG inventories, and supporting the development of management-based mitigation strategies.

Mental models of aquaculture governance in Indonesia

Aquaculture stakeholders have mental models, which are the internal cognitive representations of how they understand and prioritize the different features of their aquaculture systems. Individuals and stakeholder groups are likely to have different mental models, with implications for making cooperative governance work and guiding the rapidly emerging sector’s sustainable development. We apply a participatory approach called fuzzy cognitive mapping to capture and compare the mental models of community-based coastal pond aquaculture stakeholders in Indonesia, including farmers, government managers, and researchers who need to work together to govern a rapidly expanding aquaculture sector which faces critical sustainability challenges. To conceptually structure our comparison, we use Elinor Ostrom’s social–ecological systems framework. Our results highlight important differences between stakeholder group mental models which represent potential conflicts of interest and barriers for collaborative governance. Fish farmer models emphasize resource system challenges relating to production instability and risk, while government managers emphasize increasing production intensity to meet sectoral growth targets. Researchers, in contrast, tend to focus on pond waste treatment and water quality management. Governance attributes were consistently perceived as less frequent and less influential compared to other social–ecological dimensions, reflecting perceptions of weak governance in the sector. We identify a critical need for programs aimed at strengthening community-level institutional arrangements for governing shared aquaculture resources, increasing technical knowledge capacity, and managing financial risk. By merging all stakeholder models into a single “community” model, we identify key consensus action situations across the three groups as potential focal points for aquaculture development which may serve as a starting point for actors to work together to identify context-appropriate institutional solutions to these sustainability challenges.

Responses of zooplankton assemblages to environmental variability among brackish coastal ponds, New Zealand

Coastal brackish waters, including estuaries, lagoons and coastal ponds, experience fluctuations in physicochemical properties, particularly in salinity, due to the differential forcing of marine and freshwater inflows. Most research concerning brackish waters is skewed towards lagoons and estuaries, while relatively little exists on small coastal ponds. This study examined variability in zooplankton community composition relative to environmental conditions among brackish coastal ponds in Auckland, New Zealand. Eight coastal stormwater ponds, four freshwater ponds, and four marine sites were selected to represent a wide salinity gradient and sampled for zooplankton and environmental variables. Marked spatial and temporal variability in environmental conditions was observed among the coastal ponds. Salinity of the ponds was, on average, lower in winter, influenced by higher rainfall, while in summer reduced rainfall led to significantly lower freshwater inputs. Zooplankton communities within the coastal ponds were a mix of those in freshwater and marine sites, along with unique species not observed in each of the adjoining ecosystems. Salinity was the most important factor driving zooplankton community composition among sites, as widely reported for estuaries and lagoons. The degree of temporal change in salinity within ponds also affected community composition, with euryhaline copepods such as Sulcanus conflictus and Mesochra parva most abundant at sites with larger seasonal salinity changes. Salinity increases due to sea-level rises may lead to the disappearance of species that are less tolerant to salinity, with a move to dominance by euryhaline species.

On-farm evaluation of formulated diets on the growth and body composition of Etroplus suratensis reared in cages in low-saline coastal ponds

On-farm evaluation of formulated diets on the growth and body composition of Etroplus suratensis reared in cages in low-saline coastal ponds

Mapping the distribution and dynamics of coastal aquaculture ponds using Landsat time series data based on U2-Net deep learning model

ABSTRACT The extraction of coastal aquaculture ponds from remote sensing images is affected by the effect of ‘same object with different spectrums’ and ‘different objects with same spectrums’. The U2-Net deep learning network is able to capture more contextual information from different scales to solve this problem and is suitable for salient object detection. This study proposed a remote sensing information extraction model of coastal ponds based on U2-Net deep learning network, completed the remote sensing information extraction of coastal aquaculture ponds in Zhoushan Archipelago from 1984 to 2022, analyzed the spatiotemporal evolution of coastal aquaculture ponds in Zhoushan Archipelago. The results showed that the developed model was more accurate with a precision rate of 96.12%, a recall rate of 95.43%, and an F1-measure of 0.96. During the study period, the area of the aquaculture ponds in the Zhoushan Archipelago demonstrated an increasing trend, expanding from 471.21 hm2 in 1984–3668.55 hm2 in 2022. In addition, over half of the aquaculture ponds had been active for more than 10 years. The method developed in this study is capable of rapidly and accurately mapping coastal aquaculture ponds, and thus is significant for the management of marine resources and promoting sustainable development.

CO2 fluxes contrast between aquaculture ponds and mangrove forests and its implications for coastal wetland rehabilitation in Leizhou Peninsula, China

Coastal wetlands have great potential to mitigate climate change. However, in recent decades, the construction of aquaculture ponds has degraded coastal habitats, especially mangroves. Meanwhile, the lack of synchronized monitoring of carbon dioxide (CO2) fluxes in coastal ponds and mangroves hinders the promotion of carbon neutrality target through the implementation of coastal wetland rehabilitation. To address this issue, we deployed two eddy-covariance systems in the ponds and nearby mangroves to measure the net ecosystem CO2 exchange between atmosphere and ecosystems for two years. The results indicated that both the ponds and mangroves were CO2 sinks at the annual scale, with mean net ecosystem production (NEP) of 123 ± 39 and 1296 ± 32 g C m−2 year−1, respectively. During the 2-year period, the ponds acted as CO2 sources in certain seasons, while the mangroves displayed consistently high seasonal NEP. The construction of ponds by clearing mangroves would reduce NEP along the coasts of the Leizhou Peninsula by about 91% (96% for China), while abandoning all ponds for mangrove rehabilitation could have a significant CO2 mitigation benefit (i.e., 214.7 Gg year−1). Moreover, we compared how CO2 fluxes responded to global solar radiation and temperature by analyzing relevant parameters in the two ecosystems. Overall, the ponds showed lower light-saturated net CO2 exchange and Q10 values compared to the mangroves. Finally, we applied an advanced machine learning local interpretation algorithm to investigate the crucial drivers and their main effects on NEP. This analysis highlighted global solar radiation as the predominant driver for NEP in both ecosystems. High temperature and vapor pressure deficit inhibited mangrove NEP, particularly during summer, whereas pond NEP exhibited greater volatility in response to meteorological conditions such as temperature. Our findings provide insights for further proceeding with mangrove restoration and management to enhance the carbon sequestration capacity of coastal wetlands.

Intensity and prevalence of ectoparasites in whiteleg shrimp Litopenaeus vannamei and mud crab Scylla serrata harvested from Aceh waters Indonesia

Ectoparasite infections are a common problem in small-scale aquaculture, exerting a substantial influence on fishery production. In the context of Indonesia, the two prevalent fishery commodities are whiteleg shrimp Litopenaeus vannameii and mud crab Scylla serrata. These species are extensively cultured within Aceh province, using traditional and semi-intensive aquaculture ponds and there are no reports on ectoparasites in these two species of crustaceans. Therefore, this study aimed to analyze the intensity and prevalence of ectoparasites in mud crab and whiteleg shrimp from Aceh between August to December 2022. Mud crab samples were collected from three locations, namely Langsa City, East Aceh, and North Aceh districts, while whiteleg shrimp samples were sampled from coastal ponds in Banda Aceh, Aceh Besar, and Aceh Jaya districts. The samples were collected over five months, and a total of 300 for each species were examined microscopically by scraping the swimming legs body, and gills. Furthermore, macroscopic-sized and microscopic-sized ectoparasites were observed using stereo and binocular microscopes, respectively. The results showed that five species of ectoparasites were recorded during the study, namely Octolasmis sp., Vorticella sp., Epistylis sp., Oodinium sp., and Zoothamnium sp. Mud crab exhibited infestations of Octolasmis sp., Vorticella sp., Epistylis sp., and Oodinium sp., while whiteleg shrimp were infested by Vorticella sp., Epistylis sp., and Oodinium sp. In this study, the highest intensity for crab and shrimp was recorded in Octolasmis sp. and Epistylis sp., in November and September, respectively. The gills showed higher intensity compared to other infested organs and based on sample origin, crab and shrimp from Langsa and Banda Aceh Cities had higher results compared to other locations. The prevalence of ectoparasites exhibited a high value, reaching 100%, showing that crustacean samples were infested by ectoparasites. Therefore, the intensity of ectoparasite was varied according to sample of origin, time of sampling and infested organs. The samples of both crab and whiteleg shrimp from all locations consistently exhibited ectoparasite infestations throughout the entire study period.Keywords:Octolasmis sp.Vorticella sp.Epistylis sp.Oodinium sp.Zoothamnium sp.

Mapping China’s coastal aquaculture ponds expansion with sentinel-2 images during 2017–2021

ABSTRACT Accurately mapping large-scale areas of aquaculture ponds along China’s coastal areas is challenging. This study proposes a multi-featured decision tree method that incorporates multi-spectral indices, water inundation frequency (WIF), and object-oriented rules to extract aquaculture ponds in coastal zones using 65332 Sentinel-2 images on the GEE platform. The proposed method was validated, with the average overall accuracy of the extraction results from 2017 to 2021 reaching 90.80%, and an average F1 Score of 0.91. The results of this study indicate that the overall area of aquaculture ponds in China's coast in 2021 was 7633.83 km2, mainly located in coastal bay estuaries in Shandong Province, Jiangsu Province and Guangdong Province. In recent years, the area of coastal ponds for aquaculture in China has shown a decreasing trend, with an average annual decrease of 235.65 km2. The analysis combined with land use data shows that the ponds that have been reduced in the past five years have mainly been converted to abandoned aquaculture ponds, wetlands, and other land use types.

Assessment of marsh terrace designs for wave attenuation utilizing a wave model

The northern Gulf of Mexico is facing high rates of wetland loss due to subsidence and sea level–rise, which has encouraged the application of various wetland restoration techniques. Marsh terracing is a restoration technique that has been implemented since the early 1990 s in Texas and Louisiana, yet few studies have been conducted to evaluate its effectiveness. Marsh terraces are segmented berms of soil built in coastal ponds that were once vegetated marshes. Marsh terracing is hypothesized to dissipate wind waves, encourage marsh expansion, and reduce shoreline erosion. This study (1) assessed the effectiveness of the most common terrace shapes (linear, chevron, and square) and spacing (100, 110, and 120 m) at reducing significant wave height (Hs), (2) assessed the effectiveness of alternative terrace designs for reducing Hs during different wind conditions, and 3) estimated the construction costs of alternative terrace designs. The Simulating WAves Nearshore (SWAN) model was used to simulate wind–driven waves in ponds with real and hypothetical terrace designs. Results revealed that: (1) The chevron shape provided the greatest reduction in Hs during all wind conditions, reducing Hs by up to 54%. (2) Hs reduction was not affected by terrace spacings. (3) Based on wave attenuation, the chevron design with a 120 m terrace spacing provided the optimal outcome with an estimated construction cost/ha of $6332 in a 250,000 m2 site compared to the terrace shapes and spacings evaluated in this study. This study will help coastal managers design marsh terraces to address wetland erosion in the Gulf of Mexico and other coastal areas facing similar environmental problems.

Zooplankton Abundance and Growth of Carps in Farm-Ponds of Different Agro-Climatic Zones of Karnataka

Availability of planktons / natural fish food plays an important role in getting better growth of fish from farm ponds. Study was carried out to evaluate the zooplankton community and growth performance of Carp fishes in farm ponds of coastal and malnad agro-climatic regions of Karnataka. All the ponds were manured with cowdung and poultry manure @ 2000 kg/ha. for the production of planktons. Catla, Rohu and common carp fingerlings were stocked in all the ponds @ 10,000 nos. /ha in 1:1:1 ratio and fishes were fed with groundnut oil cake and rice bran (in 1:1 ratio) @ 5% of the body weight every day. The water samples from all the ponds were collected and filtered for zooplanktons using nylon bolting cloth (60 µm). The growth of fishes in terms of weight was recorded. The analyzed zooplankton planktons were classified into 5 class’s viz., Rotifera, Protozoa, Copepoda, Cladocera and Ostracod. Among zooplanktons observed, copepod contributed maximum to zooplankton community followed by rotifers, cladocerans and ostracod. In coastal ponds the average maximum number of zooplankton 10,368 Cells/m3 and minimum number of 176 Cells/m3 were observed. In Malnad ponds the average maximum number of zooplankton 21,797 Cells/m3 and minimum number of 1579 Cells/m3 were observed. The average maximum growth of Catla, Rohu and Common carp was observed in coastal ponds were 884.42, 640.1 and 692.27 gms respectively and in Malnad farm ponds 1080.71, 954.19 and 1023.18 gms respectively. Use of cowdung and poultry manure in combination was found useful for getting better growth in farm ponds of both the regions.

The ecology of coastal wetland ponds created by diamond mining in southern Namibia. 3. Fish

Diamond mining in southern Namibia creates seawalls that hold the ocean at bay, yet seawater overwashes or seeps through to fill landward excavated areas, forming numerous coastal ponds that reach 380 000 m2. These ponds span ages of 1–40 years, with the oldest ponds lying in the north, and the younger ponds in the central and southern areas. We investigated occupation of these mining ponds by marine fishes. The ponds offer sheltered, warm, nutrient-enriched environments, but become hypersaline after 10–12 years. The ponds contained predominantly west coast steenbras Lithognathus aureti and southern mullet Chelon richardsonii, with smaller numbers of seven other fish species, and all nine species being marine. The ichthyofauna was thus depauperate, but similar to that of periodically closed estuaries in the region. The size composition and gonadal development of both predominant species suggest they may breed in at least the younger ponds. However, in older, hypersaline, northern ponds, L. aureti transitions into an entirely female population via protandry, precluding breeding there. Body condition was low for both species in the northern ponds, and gut fullness greatest in the southern ponds. Growth of both species was faster in the ponds than in the sea, but after initially fast growth, L. aureti reached a plateau, suggesting stunting thereafter. Chelon richardsonii attained larger sizes in the ponds than in the ocean. For 10–12 years before hypersalinity sets in, the ponds constitute suitable habitat for fish. They are not estuaries as they have minimal freshwater input, but they do create conditions corresponding to closed estuaries that are otherwise scarce along this arid coastline. However, for a nursery function to be realised, the marine fish must return to the sea or else the ponds become an ‘ecological trap’.

Pengembangan Water Quality Checker untuk Tambak Budidaya Pesisir

Water Quality Checker is a water quality measuring device designed to use a microcontroller system and sensors as parameters for measuring the water quality. The aim is to facilitate the implementation of water quality monitoring from previously traditionally to using aids. The test method directly measures pH and salinity and experiments in collecting data. System workflow in tool design, Arduino orders sensors and sensor detection results are processed back to Arduino. The work results of the tool are calibrated with other standardized tools for pH and salinity values. The software used is limited to Arduino Uno and supporting devices and design applications for casing manufacturing, namely Solidwork. Using a pHE4502C sensor, a salinity sensor as a measuring tool, Arduino Uno as a microcontroller, and a LCD as a monitor that displays the value and status of the detected pH and traffic. By using the provisions that the pH value of coastal pond water is less than 6.5 which is acidic, more than 7.5 is alkaline, and the pH value is more than 6.5 and less than 7.5 which is neutral, at the time of testing it was obtained a pH value of 7.1 – 8.04 so that the solution is neutral and base. The results of the salinity sensor test for coastal pond water are 23.64 – 24.20 which indicates that this value is the normal value for brackish water salinity.

Physiological and life history responses in a mayfly (Callibaetis floridanus) inhabiting ponds with saltwater intrusion

Freshwater salinity varies in natural systems and plays a role in species distribution. Anthropogenic alterations to freshwater salinity regimes include sea level rise and subsequent intrusion of saline waters to inland habitats. While mayflies are generalized to be sensitive to increasing salinity, we still know remarkably little about the physiological processes (and their plasticity) that determine the performance of species in a changing world. Here, we explored life-history outcomes and physiological plasticity in a population of Callibaetis floridanus (Ephemeroptera: Baetidae) from a coastal pond that routinely experiences saltwater intrusion. We reared naiads from egg hatch to adulthood across a gradient of increasing salinities (113, 5,020, 9,921 μS/cm). Radiotracer flux studies (22Na, 35SO4, and 45Ca) were conducted in naiads reared at each salinity, revealing a positive association between ionic concentration and uptake rates. However, the influence of rearing history on ionic influx rates was apparent when naiads were transferred from their respective rearing water to the other experimental conditions. For example, we observed that naiads reared in the low salinity treatment (113 μS/cm) had 10.8-fold higher Na uptake rates than naiads reared at 9,921 μS/cm and transferred to 113 μS/cm. Additionally, naiads acclimated to the higher salinity water exhibited reduced uptake in ion-rich water relative to those reared in more dilute conditions (e.g., in 9,921 μS/cm water, 113 and 5,020 μS/cm acclimated naiads had 1.5- and 1.1-fold higher Na uptake rates than 9,921 μS/cm acclimated naiads, respectively). We found no significant changes in survival (80 ± 4.4%, mean ± s.e.m.) or naiad development time (24 ± 0.3 days, mean ± s.e.m.) across these treatments but did observe a 27% decrease in subimago female body weight in the most dilute condition. This reduction in female weight was associated with higher oxygen consumption rates in naiads relative to the other rearing conditions. Collectively, these data suggests that saline adapted C. floridanus may be more energetically challenged in dilute conditions, which differs from previous observations in other mayfly species.

Wavelet Analysis on Groundwater, Surface-Water Levels and Water Temperature in Doñana National Park (Coastal Aquifer in Southwestern Spain)

The Doñana National Park (DNP) is a protected area with water resources drastically diminishing due to the unsustainable extraction of groundwater for agricultural irrigation and human consumption of a nearby coastal city. In this study, we explore the potential of wavelet analysis applied to high-temporal-resolution groundwater-and-surface-water time series of temporary coastal ponds in the DNP. Wavelet analysis was used to measure the frequency of changes in water levels and water temperature, both crucial to our understanding of complex hydrodynamic patterns. Results show that the temporary ponds are groundwater-dependent ecosystems of a through-flow type and are still connected to the sand-dune aquifer, regardless of their hydrological affection, due to groundwater withdrawal. These ponds, even those most affected by pumping in nearby drills, are not perched over the saturated zone. This was proven by the evidence of a semi-diurnal (i.e., 6 h) signal in the surface-level time series of the shallow temporary ponds. This signal is, at the same time, related to the influence of the tides affecting the coastal sand-dune aquifer. Finally, we detected other hydrological processes that affect the ponds, such as evaporation and evapotranspiration, with a clear diurnal (12 h) signal. The maintenance of the ecological values and services to the society of this emblematic wetland is currently in jeopardy, due to the effect of the groundwater abstraction for irrigation. The results of this study contribute to the understanding of the behavior of these fragile ecosystems of DNP, and will also contribute to sound-integrated water-resource management.

Cutmarked bone of drought-tolerant extinct megafauna deposited with traces of fire, human foraging, and introduced animals in SW Madagascar

People could have hunted Madagascar’s megafauna to extinction, particularly when introduced taxa and drought exacerbated the effects of predation. However, such explanations are difficult to test due to the scarcity of individual sites with unambiguous traces of humans, introduced taxa, and endemic megaherbivores. We excavated three coastal ponds in arid SW Madagascar and present a unique combination of traces of human activity (modified pygmy hippo bone, processed estuarine shell and fish bone, and charcoal), along with bones of extinct megafauna (giant tortoises, pygmy hippos, and elephant birds), extirpated fauna (e.g., crocodiles), and introduced vertebrates (e.g., zebu cattle). The disappearance of megafauna from the study sites at ~ 1000 years ago followed a relatively arid interval and closely coincides with increasingly frequent traces of human foraging, fire, and pastoralism. Our analyses fail to document drought-associated extirpation or multiple millennia of megafauna hunting and suggest that a late combination of hunting, forest clearance, and pastoralism drove extirpations.

Genomes of Vibrio metoecus co-isolated with Vibrio cholerae extend our understanding of differences between these closely related species

BackgroundVibrio cholerae, the causative agent of cholera, is a well-studied species, whereas Vibrio metoecus is a recently described close relative that is also associated with human infections. The availability of V. metoecus genomes provides further insight into its genetic differences from V. cholerae. Additionally, both species have been co-isolated from a cholera-free brackish coastal pond and have been suggested to interact with each other by horizontal gene transfer (HGT).ResultsThe genomes of 17 strains from each species were sequenced. All strains share a large core genome (2675 gene families) and very few genes are unique to each species (< 3% of the pan-genome of both species). This led to the identification of potential molecular markers—for nitrite reduction, as well as peptidase and rhodanese activities—to further distinguish V. metoecus from V. cholerae. Interspecies HGT events were inferred in 21% of the core genes and 45% of the accessory genes. A directional bias in gene transfer events was found in the core genome, where V. metoecus was a recipient of three times (75%) more genes from V. cholerae than it was a donor (25%).ConclusionV. metoecus was misclassified as an atypical variant of V. cholerae due to their resemblance in a majority of biochemical characteristics. More distinguishing phenotypic assays can be developed based on the discovery of potential gene markers to avoid any future misclassifications. Furthermore, differences in relative abundance or seasonality were observed between the species and could contribute to the bias in directionality of HGT.

Mapping mineralogical heterogeneities at the nm-scale by scanning electron microscopy in modern Sardinian stromatolites: Deciphering the origin of their laminations

Stromatolites are found throughout the geological record and have received strong attention because they provide precious information about paleoenvironments and microbial paleobiodiversity. However, while this information is interpreted based on our knowledge about modern analogs, the latter remains incomplete. Here, we investigated the environmental and biological information recorded by modern stromatolites in Mari Ermi, a coastal pond in Western Sardinia that experiences severe seasonal evaporation and large salinity variations. For this purpose, we combined a variety of analytical tools, allowing to characterize the mineralogical composition of these stromatolites from the bulk, centimeter-scale to the nanometer-scale and assess the spatial distribution of the mineral phases. In particular, we used quantified x-ray elemental maps provided by energy dispersive x-ray spectrometry analyses coupled with scanning electron microscopy (SEM-EDXS). These maps were processed using an innovative data treatment allowing (i) mineral phase recognition, (ii) assessment of the mineral formula of each phase and (iii) mapping of their spatial distribution with a spatial resolution down to a hundred nanometers. Overall, this proved as an efficient approach to unravel mineralogical heterogeneities and detect informative mineral phases overlooked by bulk analyses. Mari Ermi stromatolites were mostly composed of magnesian calcite with an average Mg/Ca of ~0.1–0.2 as indicated by bulk analyses. However, microscopy observations revealed variable Mg-contents of calcite with a specific distribution, the most Mg-enriched calcites (Mg/Ca up to ~0.5) being systematically distributed around microbial remnants. Moreover, Mari Ermi stromatolites comprised an alternation of Mg-richer and Mg-poorer laminae, which paralleled the varying enrichment in microbial remnants of alternating laminae. The combination of SEM-EDXS, focused ion beam milling and transmission electron microscopy allowed to detect several minor phases, hardly or not detected at all by bulk analyses, such as aragonite, a variety of clay minerals as well as a gypsum-like phase. An additional calcium sulfate phase, best interpreted as S-apatite (cesanite), was detected by SEM-EDXS. Overall, this mineral assemblage and its definite spatial distribution record only discrete stages of the evaporation of Mari Ermi lagoon. Moreover, microorganisms seem to have a major control on Mg substitution in calcite. As a result, the dynamics of microbial populations, influenced by the salinity variations induced by evaporation in the lagoons, generates the formation of laminae in Mari Ermi stromatolites.

Grazing by an endemic atyid shrimp controls microbial communities in the Hawaiian anchialine ecosystem

AbstractAnimals often shape environmental microbial communities, which can in turn influence animal gut microbiomes. Invasive species in critical habitats may reduce grazing pressure from native species and shift microbial communities. The landlocked coastal ponds, pools, and caves that make up the Hawaiian anchialine ecosystem support an endemic shrimp (Halocaridina rubra) that grazes on diverse benthic microbial communities, including orange cyanobacterial‐bacterial crusts and green algal mats. Here, we asked how shrimp: (1) shape the abundance and composition of microbial communities, (2) respond to invasive fishes, and (3) whether their gut microbiomes are affected by environmental microbial communities. We demonstrate that ecologically relevant levels of shrimp grazing significantly reduce epilithon biomass. Shrimp grazed readily and grew well on both orange crusts and green mat communities. However, individuals from orange crusts were larger, despite crusts having reduced concentrations of key fatty acids. DNA profiling revealed shrimp harbor a resident gut microbiome distinct from the environment, which is relatively simple and stable across space (including habitats with different microbial communities) and time (between wild‐caught individuals and those maintained in the laboratory for &gt;2 yr). DNA profiling also suggests shrimp grazing alters environmental microbial community composition, possibly through selective consumption and/or physical interactions. While this work suggests grazing by endemic shrimp plays a key role in shaping microbial communities in the Hawaiian anchialine ecosystem, the hypothesized drastic ecological shifts resulting from invasive fishes may be an oversimplification as shrimp may largely avoid predation. Moreover, environmental microbial communities may have little influence on shrimp gut microbiomes.