Amphibian Communities Research Articles

Comparative efficacy of eDNA and conventional methods for monitoring wetland anuran communities

Documenting biodiversity, species occurrence, and species status require reliable monitoring techniques, but the complex life history and cryptic behavior of many anurans create challenges for conventional monitoring approaches. Environmental DNA (eDNA) surveys are a promising alternative (or complement) to conventional anuran monitoring, but their relative success has not been fully tested. We assessed the comparative efficacy of targeted eDNA detection via quantitative PCR (qPCR) and three conventional amphibian survey methods (visual encounter, breeding call, and larval dipnet surveys) for detecting nine anuran species in natural wetlands in southern Ontario, Canada. Our analyses revealed that all assessment methods yielded imperfect detection, with visual encounter and eDNA surveys detecting the greatest species richness and eDNA surveys requiring the fewest sampling events. Amphibian community composition results differed among survey methods and sampling events, and detection efficacy was markedly variable, with some species requiring two to three methods to maximize detection success. Notably, two relatively terrestrial species (Anaxyrus americanusandHyla versicolor) had relatively low and seasonally variable eDNA detection rates, suggesting that species-specific ecology likely affects eDNA presence or detection. These findings suggest that optimized monitoring for complex anuran communities may require application of multiple monitoring methods, which may need to be tailored to individual target species or communities.

Difficult times for amphibians: Effects of land-use change at the local and landscape scales in the Iberá Wetlands

Land-use change and management practices have led to habitat loss, one of the greatest factors in biodiversity decline. Particularly, amphibians comprise the highest number of threatened vertebrate species at the global scale. In this work, amphibian communities were analysed in three differing landscapes: a protected wetland, a livestock-impaired rangeland and a pine afforestation. In each landscape, amphibian species were sampled. Land-cover type and composition, as well as primary vegetation types were characterised at the landscape and local scale, respectively. The relationship between these environmental variables and the amphibian communities was analysed. Twenty-one amphibian species were identified; the protected and afforested landscapes were the richest, whereas the rangeland showed the lowest species richness and diversity estimates. At the local scale, vegetation, water coverage and land-use category explained the higher presence of amphibian species and their abundance. These results show how different land-uses, especially livestock farming, modify the composition of amphibian communities. This work constitutes a foundation for the development of sustainable management practices for conserving amphibians in landscape-level altered habitats.

Evolutionary ecology of host competence after a chytrid outbreak in a naive amphibian community.

Naive multi-host communities include species that may differentially maintain, transmit and amplify novel pathogens; therefore, we expect species to fill distinct roles during infectious disease emergence. Characterizing these roles in wildlife communities is challenging because most disease emergence events are unpredictable. Here, we used field-collected data to investigate how species-specific attributes influenced the degree of exposure, probability of infection, and pathogen intensity, during the emergence of the fungal pathogen Batrachochytrium dendrobatidis (Bd) in a highly diverse tropical amphibian community. Our findings confirmed that ecological traits commonly evaluated as correlates of decline were positively associated with infection prevalence and intensity at the species level during the outbreak. We identified key hosts that disproportionally contributed to transmission dynamics in this community and found a signature of phylogenetic history in disease responses associated with increased pathogen exposure via shared life-history traits. Our findings establish a framework that could be applied in conservation efforts to identify key species driving disease dynamics under enzootics before reintroducing amphibians back into their original communities. Reintroductions of supersensitive hosts that are unable to overcome infections will limit the success of conservation programmes by amplifying the disease at the community level. This article is part of the theme issue 'Amphibian immunity: stress, disease and ecoimmunology'.

Broad host susceptibility of North American amphibian species to Batrachochytrium salamandrivorans suggests high invasion potential and biodiversity risk

Batrachochytrium salamandrivorans (Bsal) is a fungal pathogen of amphibians that is emerging in Europe and could be introduced to North America through international trade or other pathways. To evaluate the risk of Bsal invasion to amphibian biodiversity, we performed dose-response experiments on 35 North American species from 10 families, including larvae from five species. We discovered that Bsal caused infection in 74% and mortality in 35% of species tested. Both salamanders and frogs became infected and developed Bsal chytridiomycosis. Based on our host susceptibility results, environmental suitability conditions for Bsal, and geographic ranges of salamanders in the United States, predicted biodiversity loss is expected to be greatest in the Appalachian Region and along the West Coast. Indices of infection and disease susceptibility suggest that North American amphibian species span a spectrum of vulnerability to Bsal chytridiomycosis and most amphibian communities will include an assemblage of resistant, carrier, and amplification species. Predicted salamander losses could exceed 80 species in the United States and 140 species in North America.

Integrated analysis shows how the effects of extreme flooding events propagate through fish communities to impact amphibians.

Research Highlight: Davis, C. L., Walls, S. C., Barichivich, W. J., Brown, M. E., & Miller, D. A. (2022). Disentangling direct and indirect effects of extreme events on coastal wetland communities. Journal of Animal Ecology, https://doi.org/10.1111/1365-2656.13874. Catastrophic events such as floods, hurricanes, winter storms, droughts and wildfires increasingly touch our lives either directly or indirectly. These events draw our attention to the seriousness of changes in climate not only to human well-being but also to the integrity of ecological systems upon which we depend. Understanding the impacts of extreme events on ecological systems requires the ability to characterize the cascading effects of environmental changes on the environments in which organisms live and the altered biological interactions produced. This scientific ambition represents no small challenge for the study of animal communities, which are typically difficult to census as well as dynamic in time and space. Davis et al. (2022) in a recent study in the Journal of Animal Ecology examined the amphibian and fish communities found in depressional coastal wetlands to better understand how they respond to major rainfall and flooding events. Data from the U.S. Geological Survey's Amphibian Research and Monitoring Initiative provided an 8-year record of observations as well as environmental measurements. For this study, the authors integrated techniques for assessing the dynamics of animal populations with a Bayesian implementation of structural equation modelling. Using their integrated methodological approach permitted the authors to reveal the direct and indirect effects of extreme weather events on co-occurring amphibian and fish communities while accounting for observational uncertainty and temporal variation in population-level processes. Their findings indicate that the most prominent effects of flooding on the amphibian community were caused by changes in the fish community that led to increased predation and resource competition. In their conclusions, the authors emphasize the importance of understanding networks of abiotic and biotic effects if we are to predict and mitigate the influence of extreme weather events.

Patterns in usage of under-road tunnels by an amphibian community highlights the importance of tunnel placement and design for mitigation

Patterns in usage of under-road tunnels by an amphibian community highlights the importance of tunnel placement and design for mitigation

Hydrology is a major influence on amphibian abundance in a large European floodplain.

River-floodplain ecosystems play a crucial role in connecting landscape patches through hydrological connectivity, but they are among the most threatened ecosystems. Floodplains provide important habitat for amphibians by connecting aquatic and terrestrial habitats. Modifications to floodplain hydrology can impact amphibian communities, yet few studies have examined amphibian metacommunities in floodplain wetlands.In this study, we assessed patterns in amphibian breeding abundance in one of the largest floodplains of the Danube River, Hungary, relative to hydrological connectivity and multi-scale variables at 30 waterbody sites. Our aim was to determine whether these patterns aligned with the pond-permanence gradient hypothesis, where breeding amphibian abundance is predicted to be highest in ephemeral ponds without large predatory fish. We used Bayesian hierarchical modelling to estimate multi-species abundance from repeated survey (count) data collected over one breeding season.We detected the eggs and larvae of four amphibian species. The best model of abundance included covariates describing two principal component axes associated with waterbody hydrology and landscape composition within a 500-m radius of a site. There was a positive relationship between mean community abundance at a site and hydrological disconnection from the main river channel; however, the common toad (Bufo bufo) was associated with hydrologically connected waterbodies. There was a positive relationship between mean community abundance and a high proportion of forest cover and low cover of agricultural land within a 500-m radius around a site, although this relationship was clear for only two species. There was no support for models containing the number of large predatory fish species detected at a site.Although our results showed that amphibian abundance declined with hydrological connectivity, based on model selection we could not ascribe this relationship to an increased number of large predatory fish species detected in waterbodies close to the main river channel. Differences in life history and habitat requirements are likely to have explained interspecific responses to hydrological connectivity. Our results underscore the importance of addressing amphibian abundance at multiple spatial scales in floodplain wetlands, as landscape composition partly explained patterns in abundance.Application of multi-species abundance modelling allowed us to investigate environmental relationships for common and infrequently detected species. Habitat restoration programmes in floodplains should provide waterbodies disconnected from main river channels as potential amphibian breeding sites and protect or restore forest as terrestrial habitat.

Some like it salty: Spatio‐temporal dynamics of salinity differentially affect anurans and caudates in coastal wetlands

Abstract Coastal wetlands are naturally subjected to salinity, which is expected to increase through global climate changes. Most species will be affected by these changes, leading to major consequences for community structure and ecosystem functioning. We investigated variation of salinity of temporary wetlands across spatial (1,000 m from the ocean) and temporal (across three breeding season) scales relevant to coastal biodiversity and used amphibians (six species, sampled across one breeding season) as a model to investigate the consequences of the spatio‐temporal variation of salinity in 24 ponds situated on the Atlantic coast of France. We show that salinity is a highly dynamic environmental variable that varies widely both across spatial and temporal scales. The spatio‐temporal dynamics of salinity are a critical factor structuring amphibian communities that affect the main amphibian phylogenetic groups (caudates vs. anurans) differently. Temporal variation in salinity disrupts the match between salinity selected by reproductive adults and those experienced later by their developing offspring, which negatively affect reproductive success. Future changes in coastal salinity are likely to affect the structure and functioning of these ecosystems, excluding salt‐intolerant species and eventually leading to less diverse communities of salt‐tolerant species.

Environmental Factors Affecting Amphibian Communities in River Basins of the Southern Apennines

The study of the environmental features affecting amphibian communities is a priority task for addressing effective conservation initiatives. In the southern edge of the Apennines (Sila Massif, Calabria Region, Italy), we surveyed the distribution of amphibians in lotic freshwater habitats (eight rivers, 17 sampling stations, 87 transects) and recorded nine environmental variables, including the occurrence of potential predators (fish and Eurasian otter Lutra lutra), potentially affecting the distribution and breeding success of amphibian species. A total of seven amphibian species was recorded (75.9% of transects). Fish occurred in all rivers while the otter was found in four rivers (Amato, Lese, Neto, and Savuto). Illuminance and bank heterogeneity were the main factors affecting amphibian reproduction, while neither otter nor fish presence showed significant effects on the amphibian community. Overall, habitat complexity and coevolution history seemed to shape the distribution of amphibians and their breeding sites, while the ongoing recolonization of the study area by the otter is expected to have a negligible impact on the richness of the amphibian community.

Severe wildfires promoted by climate change negatively impact forest amphibian metacommunities

AbstractAimChanges to the extent and severity of wildfires driven by anthropogenic climate change are predicted to have compounding negative consequences for ecological communities. While there is evidence that severe weather events like drought impact amphibian communities, the effects of wildfire on such communities are not well understood. The impact of wildfire on amphibian communities and species is likely to vary, owing to the diversity of their life‐history traits. However, no previous research has identified commonalities among the amphibians at most risk from wildfire, limiting conservation initiatives in the aftermath of severe wildfire. We aimed to investigate the impacts of the unprecedented 2019–2020 black summer bushfires on Australian forest amphibian communities.LocationEastern coast of New South Wales, Australia.MethodsWe conducted visual encounter surveys and passive acoustic monitoring across 411 sites within two regions, one in northeast and one in southeast New South Wales. We used fire severity and extent mapping in two multispecies occupancy models to assess the impacts of fire on 35 forest amphibian species.ResultsWe demonstrate a negative influence of severe fire extent on metacommunity occupancy and species richness in the south with weaker effects in the north—reflective of the less severe fires that occurred in this region. Both threatened and common species were impacted by severe wildfire extent. Occupancy of burrowing species and rain forest specialists had mostly negative relationships with severe wildfire extent, while arboreal amphibians had neutral relationships.Main ConclusionMetacommunity monitoring and adaptive conservation strategies are needed to account for common species after severe climatic events. Ecological, morphological and life‐history variation drives the susceptibility of amphibians to wildfires. We document the first evidence of climate change‐driven wildfires impacting temperate forest amphibian communities across a broad geographic area, which raises serious concern for the persistence of amphibians under an increasingly fire‐prone climate.

A 91% decline in a common anuran in an otherwise stable amphibian community inferred from 17 years of rapid road surveys

AbstractAmphibians are disproportionately represented among the many vertebrate taxa that are declining globally. Few long‐term studies of amphibians exist, especially in temperate climates, hindering our understanding of long‐term trends in amphibian communities, which may delay or prevent management action. Here, we develop and deploy an inexpensive monitoring method with potentially broad scientific and community uptake, ‘rapid road surveys’. We test whether this protocol is useful in understanding relative abundance in an amphibian community over a 17‐year period. From 2003 to 2019, we performed thousands of rapid (5–15 min) amphibian surveys and recorded the number of on‐road amphibians along a single, 267 m stretch of secondary roads in rural Canada. Assuming that on‐road occurrence reflects relative amphibian population sizes, we show that amphibians have declined by approximately 73% from 2003 to 2019. The decline was driven by a remarkable 91% decrease in the abundance of northern leopard frogs (Lithobates pipiens), the species comprising the most observation records, while all other species did not show a temporal trend. We cannot attribute a definitive mechanism to the L. pipiens decline. However, by ruling out a number of putative causes, we hypothesize that it may be related to land‐use change or infectious disease. Our results show that a simple, temporally replicated road survey protocol, deployed in a spatially restricted area, can be a valuable tool for conservation scientists to understand trends in abundance across an entire community. We discuss how these rapid road surveys are likely a viable option for future community science initiatives.

Taxonomic and functional diversity of the amphibian and reptile communities of the state of Durango, Mexico

Taxonomic and functional diversity of the amphibian and reptile communities of the state of Durango, Mexico

Paleoenvironments and climate at Nahal Me'arot (Mount Carmel, Israel) during the Middle and Late Pleistocene: The herpetofauna of Tabun Cave and el-Wad Terrace

The Paleolithic record of the Levant encompasses several key changes in human population dynamics and human biological and cultural evolution. These processes are frequently linked to climatic shifts, but high-resolution and long-term paleoenvironmental and paleoclimatic records often come from off-site sources, hindering the correlation with human developments observed in the archaeological sites. This paper aims to reconstruct the long-term paleoenvironmental and paleoclimatic records of the Middle and Late Pleistocene Nahal Me'arot, Mount Carmel, Israel, using the archaeological herpetofauna assemblages from the Middle Paleolithic (MP) of Tabun Cave (layers C and B; using 18 stratigraphically ordered beds in total) and the Early Natufian of el-Wad Terrace (EWT), and employing the habitat weighting and mutual climate range methods. To strengthen our control of the correlation between the observed variation and the changing environment we also add a modern sample from the same location. We provide a systematic description of the finds and employ taphonomic and taxonomic analyses, which enabled us to identify three major accumulation agents that differentially affected the various samples: raptor predation predominantly in Tabun C, natural entrapment and death in Tabun B, and human consumption in Natufian EWT.The studied Tabun sequence exhibits changes in temperature and humidity. These are more apparent in the lower part (Tabun C), where the driest spell of our sequence also occurred, than in its upper part (Tabun B), and potentially coincide with the succession of two different hominin populations in the site. The correlation with regional off-site records remains challenging. Yet, given the available dates for the layers immediately underlying our driest sample, this dry fluctuation can be cautiously correlated with one of the dry phases apparent in the isotope records at the end of MIS 6. In the Terminal Pleistocene, the Early Natufian EWT reconstruction shows a wetter and cooler climate than the present day, with favorable Eastern Mediterranean vegetation, possibly enabling the long-term sedentary habitation that is suggested for this phase. Finally, our results testify to the general resilience of amphibian and reptile communities through the sequence but also to the rising impact of human activities on the reptile community during the Natufian.

Amphibians of Rwanda: Diversity, Community Features, and Conservation Status

The diversity and distribution of the amphibians in Rwanda was critically reviewed to provide a reliable species inventory for informed conservation management. The checklist of the amphibian species of Rwanda is based on results of our own fieldwork, historical records compiled from the literature, and examination of voucher specimens in museum collections. A total of 62 species are recorded, and 22 further species listed in field guides and open-access data bases are discussed, identified as erroneous records, and consequently not included in the country list. We provide diagnostic characters of external morphology and the advertisement call for each validated species, and a short synopsis of geographic distribution, altitudinal range, occurrence in the provinces of Rwanda, and habitat preference. We provide keys to all genera, and all taxonomically described species based on morphological characters and additional keys based on features of the advertisement calls. We discuss features of amphibian communities including local community structure and delimitation of altitudinal metacommunities. Based on the IUCN red list assessment and our field surveys, we propose for the first time a national red list of amphibians in Rwanda.

Geographically Isolated Wetlands as a Reserve for the Conservation of Amphibian Biodiversity at the Edge of Their Range

Wetlands are of great importance for biodiversity and nature conservation, especially geographically isolated wetlands (GIW). Yet literature about the ecological value of such GIW is missing, especially at the edge of the distribution of endangered species such as amphibians. In 2018 and 2022, we monitored amphibian communities in 15 isolated (GIW) and 12 non-isolated (nGIW) ponds by counting individuals using three methods: (1) capturing with hand nets, (2) visual counting, and (3) capturing with fyke traps. The three methods provided similar results, showing the great importance of GIW for amphibians, especially newts, whose abundance was 5–13 times greater in GIW compared to nGIW. The largest numbers of species and individuals (adults and larvae) were found in isolated wetlands (GIW). In non-isolated water bodies (nGIW) where more than 10 individuals of the Chinese sleeper Perccottus glenii, an alien invasive fish, were found, amphibians were not found at all. Importantly, between 2018 and 2022, the northern crested newt, T. cristatus, dramatically decreased in the nGIW. As a result of our work, it was revealed that the reconstruction of geographically isolated wetlands is very important for the conservation of amphibian biodiversity in a changing climate. One of the most effective measures aimed at protecting amphibians from negative factors—the spread of alien invasive fish species and diseases—is the reconstruction of wetlands in historically exploited landscapes with the creation of a wide range of water bodies yet broadly dominated by geographically isolated ponds.

Experimental evaluation of how biological invasions and climate change interact to alter the vertical assembly of an amphibian community.

While biotic-abiotic interactions are increasingly documented in nature, a process-based understanding of how such interactions influence community assembly is lacking in the ecological literature. Perhaps the most emblematic and pervasive example of such interactions is the synergistic threat to biodiversity posed by climate change and invasive species. Invasive species often out-compete or prey on native species. Despite this long-standing and widespread issue, little is known about how abiotic conditions, such as climate change, will influence the frequency and severity of negative biotic interactions that threaten the persistence of native fauna. Treefrogs are a globally diverse group of amphibians that climb to complete life-cycle processes, such as foraging and reproduction, as well as to evade predators and competitors, resulting in frog communities that are vertically partitioned. Furthermore, treefrogs adjust their vertical position to maintain optimal body temperature and hydration in response to environmental change. Here, utilizing this model group, we designed a novel experiment to determine how extrinsic abiotic and biotic factors (changes to water availability and an introduced predator, respectively) interact with intrinsic biological traits, such as individual physiology and behaviour, to influence treefrogs' vertical niche. Our study found that treefrogs adjusted their vertical niche through displacement behaviours in accordance with abiotic resources. However, biotic interactions resulted in native treefrogs distancing themselves from abiotic resources to avoid the non-native species. Importantly, under altered abiotic conditions, both native species avoided the non-native species %- more than they avoided their native counterpart. Additionally, exposure to the non-native species resulted in native species altering their tree climbing behaviours by and becoming more vertically dynamic to avoid the non-native antagonist. Our experiment determined that vertical niche selection and community interactions were most accurately represented by a biotic-abiotic interaction model, rather than a model that considers these factors to operate in an isolated (singular) or even additive manner. Our study provides evidence that native species may be resilient to interacting disturbances via physiological adaptations to local climate and plasticity in space-use behaviours that mediate the impact of the introduced predator.

Amphibian decline in a Central European forest and the importance of woody debris for population persistence

Achieving an understanding of species’ temporal and spatial abundance patterns is a prerequisite for proper conservation and management decisions. Little is known of the ecological indicators of census size or biomass of terrestrial amphibian communities and historical estimates of population size are rare. Here we took advantage of abundance and biomass data collected in 1967/1968 for a leaf-litter amphibian community in Niepołomice Forest (NF) in south-central Poland. Using the same technique (removal sampling), we censused the amphibian community of this forest 50 years later (2016/2017), spatially matching a subset of current plots with the historical sampling sites. Averaged over all plots, we revealed at least a fourfold decline in amphibian abundance from 2817 ± 776 individuals/ha in 1967 to 674 ± 508 individuals/ha currently, paralleled by a decline in biomass from roughly 15.5 ± 1.7 to 3.8 ± 3.1 kg/ha. The decline was more striking (over 15-fold) for current plots placed in the same forest division as the historical plots (mean counts of 157 ± 103 individuals/ha corresponding in biomass to 1.0 ± 0.5 kg/ha). We also recorded a change in species composition between surveys, and propose that conversion of aquatic habitat and forest succession have decreased amphibian diversity and abundance in NF. Further, we estimated densities of anuran amphibians in forest plots differing in management regime and local habitat characteristics for contemporary plots (all historical plots were placed in managed forest). We found that unmanaged, old growth forest plots with coarse woody debris on the forest floor held on average twice as many anurans compared to plots in managed stands. Average body condition of the most common species, Rana temporaria, measured as a scaled mass index, was enhanced in plots situated in old growth forest. Our findings suggest that the preservation of old growth forests containing coarse woody debris may boost anuran abundance, biomass and body condition, and has the potential to buffer against long-term demographic decline. Moreover, the retention of deadwood could be a means of increasing the conservation potential of managed forests for terrestrial amphibian communities.

Amphibian communities along a forest degradation gradient in an East African forest reserve

The amphibian communities in Africa's tropical forests are of global conservation importance, but disturbances derived from anthropological activities threaten to dismantle this irreplaceable diversity. We explored the impacts of forest degradation on the amphibian community in Mabira Central Forest Reserve, Uganda. We sampled amphibians from March to July of 2015 in plots that were positioned along a gradient of forest degradation. We conducted visual encounter surveys across three categories of forest degradation with six 300-m transects in each (four surveys per transect). From 216 h of surveyor effort, we detected 3563 individual frogs representing 30 species from eight families and 13 genera. Hyperoliidae was the most diverse family represented by 13 species in four genera. Hyperolius had the highest number of species (nine) followed by four genera each represented by three species (Phrynobatrachus, Pytchadena, Leptopelis, and Sclerophrys). Comparisons among plots along a gradient of forest degradation revealed differences in species richness, composition, and frequency of encounters. The regenerating and degraded forest plots were similar in species composition to each other and were dominated by mostly widespread, open-canopy species. Several forest-dependent species were recorded in both the regenerating and mature forest plots but were absent from the degraded plots. In the regenerating and mature forests, species presence was significantly associated with high canopy cover, high relative humidity, and dense leaf litter, whereas the microhabitat variables of high grass cover and high temperature were most influential in the degraded forests. Our study provides important data on an Afrotropical amphibian community and suggests that forest degradation has dramatically altered the habitat to the detriment of forest specialist species.

Elevated alpha diversity in disturbed sites obscures regional decline and homogenization of amphibian taxonomic, functional and phylogenetic diversity

Loss of natural habitat due to land-use change is one of the major threats to biodiversity worldwide. It not only affects the diversity of local species communities (alpha diversity) but can also lead to large-scale homogenization of community composition (reduced beta diversity) and loss of regional diversity (gamma diversity), but these effects are still rarely investigated. We assessed the impact of land-use change on taxonomic, functional and phylogenetic diversity of amphibians in Rwanda, both on the local (community-level) and regional scale (country-wide). Alpha diversity in local communities was higher in farmland than in natural habitats; however, species turnover among farmland sites was much lower than among natural sites, resulting in highly homogenized communities and reduced taxonomic, functional and phylogenetic gamma diversity in farmland across Rwanda. Amphibians found in farmland were mostly disturbance-tolerant species that are widespread in eastern Africa and beyond. In contrast, most of the regionally endemic frog species that make this region a continent-wide hotspot of amphibian diversity were found only in the natural habitats. Ongoing habitat conversion might result in further homogenization of amphibian communities across sub-Saharan Africa and the loss of regional endemism, unique evolutionary lineages, and multifunctionality.

Disentangling direct and indirect effects of extreme events on coastal wetland communities.

One of the primary ways in which climate change will impact coastal freshwater wetlands is through changes in the frequency, intensity, timing and distribution of extreme weather events. Disentangling the direct and indirect mechanisms of population- and community-level responses to extreme events is vital to predicting how species composition of coastal wetlands will change under future conditions. We extended static structural equation modelling approaches to incorporate system dynamics in a multi-year multispecies occupancy model to quantify the effects of extreme weather events on a coastal freshwater wetland system. We used data from an 8-year study (2009-2016) on St. Marks National Wildlife Refuge in Florida, USA, to quantify species-specific and community-level changes in amphibian and fish occupancy associated with two flooding events in 2012 and 2013. We examine how physical changes to the landscape, including potential changes in salinity and increased wetland connectivity, may have contributed to or exacerbated the effects of these extreme weather events on the biota of isolated coastal wetlands. We provide evidence that the primary effects of flooding on the amphibian community were through indirect mechanisms via changes in the composition of the sympatric fish community that may have had lethal (i.e. through direct predation) or non-lethal (i.e. through direct or indirect competitive interactions) effects. In addition, we have shown that amphibian species differed in their sensitivity to direct flooding effects and indirect changes in the fish community and wetland-specific conductance, which led to variable responses across the community. These effects led to the overall decline in amphibian species richness from 2009 to 2016, suggesting that wetland-breeding amphibian communities on St. Marks National Wildlife Refuge may not be resilient to predicted changes in coastal disturbance regimes because of climate change. Understanding both direct and indirect effects, as well as species interactions, is important for predicting the effects of a changing climate on individual species, communities and ecosystems.