Unfolding the dynamics of ecosystems undergoing alternating wet-dry transitional states

A significant fraction of Earth's ecosystems undergoes periodic wet-dry alternating transitional states. These globally distributed water-driven transitional ecosystems, such as intermittent rivers and coastal shorelines, have traditionally been studied as two distinct entities, whereas they constitute a single, interconnected meta-ecosystem. This has resulted in a poor conceptual and empirical understanding of water-driven transitional ecosystems. Here, we develop a conceptual framework that places the temporal availability of water as the core driver of biodiversity and functional patterns of transitional ecosystems at the global scale. Biological covers (e.g., aquatic biofilms and biocrusts) serve as an excellent model system thriving in both aquatic and terrestrial states, where their succession underscores the intricate interplay between these two states. The duration, frequency, and rate of change of wet-dry cycles impose distinct plausible scenarios where different types of biological covers can occur depending on their desiccation/hydration resistance traits. This implies that the distinct eco-evolutionary potential of biological covers, represented by their trait profiles, would support different functions while maintaining similar multifunctionality levels. By embracing multiple alternating transitional states as interconnected entities, our approach can help to better understand and manage global change impacts on biodiversity and multifunctionality in water-driven transitional ecosystems, while providing new avenues for interdisciplinary studies.

Global patterns of allochthony in stream-riparian meta-ecosystems

Ecosystems that are coupled by reciprocal flows of energy and nutrient subsidies can be viewed as a single "meta-ecosystem." Despite these connections, the reciprocal flow of subsidies is greatly asymmetrical and seasonally pulsed. Here, we synthesize existing literature on stream-riparian meta-ecosystems to quantify global patterns of the amount of subsidy consumption by organisms, known as "allochthony." These resource flows are important since they can comprise a large portion of consumer diets, but can be disrupted by human modification of streams and riparian zones. Despite asymmetrical subsidy flows, we found stream and riparian consumer allochthony to be equivalent. Although both fish and stream invertebrates rely on seasonally pulsed allochthonous resources, we find allochthony varies seasonally only for fish, being nearly three times greater during the summer and fall than during the winter and spring. We also find that consumer allochthony varies with feeding traits for aquatic invertebrates, fish, and terrestrial arthropods, but not for terrestrial vertebrates. Finally, we find that allochthony varies by climate for aquatic invertebrates, being nearly twice as great in arid climates than in tropical climates, but not for fish. These findings are critical to understanding the consequences of global change, as ecosystem connections are being increasingly disrupted.

Ecosystem bioelement variability is associated with freshwater animal aggregations at the aquatic-terrestrial interface

The impacts of animals on the biogeochemical cycles of major bioelements like C, N, and P are well-studied across ecosystem types. However, more than 20 elements are necessary for life. The feedbacks between animals and the biogeochemical cycles of the other bioelements are an emerging research priority. We explored how much freshwater mussels (Bivalvia: Unionoida) were related to variability in ecosystem pools of 10 bioelements (Ca, Cu, Fe, K, Mn, Na, Mg, P, S and Zn) in streams containing a natural mussel density gradient in the US Interior Highlands. We studied the concentrations of these bioelements across the aquatic-terrestrial interface-in the porewater of riverine gravel bars, and the emergent macrophyte Justicia americana. Higher mussel density was associated with increased calcium in gravel bars and macrophytes. Mussel density also correlated with variability in iron and other redox-sensitive trace elements in gravel bars and macrophytes, although this relationship was mediated by sediment grain size. We found that two explanations for the patterns we observed are worthy of further research: (1) increased calcium availability in gravel bars near denser mussel aggregations may be a product of the buildup and dissolution of shells in the gravel bar, and (2) mussels may alter redox conditions, and thus elemental availability in gravel bars with fine sediments, either behaviorally or through physical structure provided by shell material. A better understanding of the physical and biogeochemical impacts of animals on a wide range of elemental cycles is thus necessary to conserve the societal value of freshwater ecosystems.

Effects of municipal wastewater effluents on the digestive gland microbiome of wild freshwater mussels (Lasmigona costata)

Gut microbial communities are vital for maintaining host health, and are sensitive to diet, environment, and chemical exposures. Wastewater treatment plants (WWTPs) release effluents containing antimicrobials, pharmaceuticals, and other contaminants that may negatively affect the gut microbiome of downstream organisms. This study investigated changes in the diversity and composition of the digestive gland microbiome of flutedshell mussels (Lasmigona costata) from upstream and downstream of two large (service >100,000) WWTPs. Mussel digestive gland microbiome was analyzed following the extraction, PCR amplification, and sequencing of bacterial DNA using the V3-V4 hypervariable regions of the 16 S rRNA gene. Bacterial alpha diversity decreased at sites downstream of the second WWTP and these sites were dissimilar in beta diversity from sites upstream and downstream of the first upstream WWTP. The microbiomes of mussels collected downstream of the first WWTP had increased relative abundances of Actinobacteria, Bacteroidetes, and Firmicutes, with a decrease in Cyanobacteria, compared to upstream mussels. Meanwhile, those collected downstream of the second WWTP increased in Proteobacteria and decreased in Actinobacteria, Bacteroidetes, and Tenericutes. Increased Proteobacteria has been linked to adverse effects in mammals, but their functions in mussels is currently unknown. Finally, effluent-derived bacteria were found in the microbiome of mussels downstream of both WWTPs but not in those from upstream. Overall, results show that the digestive gland microbiome of mussels collected upstream and downstream of WWTPs differed, which has implications for altered host health and the transport of WWTP-derived bacteria through aquatic ecosystems.

Understanding the influence of multiple pollutant stressors on the decline of freshwater mussels in a biodiversity hotspot

The Clinch River watershed of the upper Tennessee River Basin of Virginia and Tennessee, USA supports one of North America's greatest concentrations of freshwater biodiversity, including 46 extant species of native freshwater mussels (Order Unionida), 20 of which are protected as federally endangered. Despite the global biological significance of the Clinch River, mussel populations are declining in some reaches, both in species richness and abundance. The aim of this study was to evaluate the exposure of adult resident mussels to a suite of inorganic and organic contaminant stressors in distinct sections of the Clinch River that encompassed a range of mussel abundance and health. To provide insight into the potential role of pollutants in the decline of mussels, including within a previously documented "zone of mussel decline", the mainstem Clinch River (8 sites) and its tributaries (4 sites) were examined over two consecutive years. We quantified and related metals and organic contaminant concentrations in mussels to their associated habitat compartments (bed sediment, suspended particulate sediment, pore water, and surface water). We found that concentrations of organic contaminants in resident mussels, particularly the suite of 42 polycyclic aromatic hydrocarbons (PAHs) analyzed, were related to PAH concentrations in all four habitat (media) compartments. Further, PAH concentrations in mussel tissue (range 37.8-978.1 ng/g dry weight in 2012 and 194.3-1073.7 ng/g dry weight in 2013) were negatively related to the spatial pattern in mussel densities (r_s = -0.64, p ≤ 0.05 in 2012 and r_s = -0.83, p ≤ 0.05 in 2013) within the river, and were highest in the "zone of mussel decline". In contrast, the suite of 22 metals analyzed in resident mussels were largely unrelated to the spatial pattern of variation of metals in the four habitat compartments except for Manganese (Mn; range 3630.5-23,749.2 μg/g dry weight in 2012 and 1540.4-12,605.8 μg/g dry weight in 2013) in surface water (r_s = 0.58, p < 0.1) and pore water (r_s = 0.76, p ≤ 0.05). This study revealed that PAHs and Mn are important pollutant stressors to mussels in the Clinch River and that they are largely being delivered through the Guest River tributary watershed. Accordingly, future conservation and management efforts would benefit by identifying, and ideally mitigating, the sources of PAHs, Mn, and other current or legacy mining-associated pollutants to the mainstem river and its tributaries.

Filter-feeders have differential bottom-up impacts on green and brown food webs

Nutrient recycling by consumers can strongly impact nutrient availability for autotrophic and heterotrophic microbes, thus impacting functions such as primary production and decomposition. Filter-feeding freshwater mussels form dense, multispecies assemblages in aquatic ecosystems and have been shown to play a critical role in nutrient cycling. Mussel excretion can enhance benthic primary production and influence algal species composition. However, the role of mussels in brown or detritus-based food webs and species-specific differences has received considerably less attention. Here, using mesocosm experiments, we assessed how three species of freshwater mussels that occupy three different phylogenetic tribes influenced benthic algal accrual, ecosystem metabolism, cotton strip decomposition, leaf litter (Acer saccharum) decomposition, and litter-associated fungal biomass measured as ergosterol. Additionally, we measured mussel excretion and biodeposition rates and assessed the stoichiometry (C:N, C:P, and N:P) of the benthic algae, cotton strips, and leaf litter. In comparison to controls without mussels, generally, mussel treatments had higher benthic algal biomass composed of more diatoms, higher gross primary productivity and net ecosystem production rates, and higher cotton strip tensile strength loss, but there was not a difference in ecosystem respiration rates, leaf litter decomposition rates, or fungal biomass. Benthic algae had lower C:N and higher N:P in mussel treatment tanks and cotton strip C:N was lower in mesocosms with mussels. Our results suggest that nutrient regeneration by mussels most strongly regulates green food webs, with some impacts to brown food webs, suggesting that consumers have interactive effects on microbial functioning in freshwaters.

Riparian condition influences spider community structure and the contribution of aquatic carbon subsidies to terrestrial habitats

Degradation of riparian zones can alter aquatic and terrestrial communities of flora and fauna and disrupt their role in assimilating and mobilising carbon between the two ecosystems. Riparian spiders that predate on emergent aquatic invertebrates can contribute to carbon flux and the structure of aquatic and riparian food webs. The impact of riparian degradation on spiders in temperate rivers of Australia and their role in this broader ecosystem function is poorly understood. We surveyed the riparian zone of four rivers of south-western Australia in areas of natural intact vegetation and degraded agricultural land to explore whether riparian spider abundance, and diversity may be affected by changes to riparian condition. We also assessed the impact of the riparian condition on carbon fluxes between aquatic and terrestrial environments, using stable isotope analysis. We found overall abundance of riparian spiders was higher in degraded agricultural sites compared to natural intact sites and the structure of spider assemblages was different. Orb-weaver spiders (Araneidae and Tetragnathidae) were found to be more abundant in agricultural areas where canopy cover and understory are sparse as a result of livestock grazing and trampling. The contribution of carbon from aquatic invertebrates in a natural intact site was 48.5% for Orb-weavers and 41.6% for Cursorial Hunter spiders but reduced to 19.6% and 39.9% respectively in a degraded agricultural site. These results suggest that the position of spiders in riparian food webs and the amount of aquatic subsidy may change according to the condition and complexity of the riparian zone.

Toward spatio-temporal delineation of positive interactions in ecology

Given unprecedented rates of biodiversity loss, there is an urgency to better understand the ecological consequences of interactions among organisms that may lost or altered. Positive interactions among organisms of the same or different species that directly or indirectly improve performance of at least one participant can structure populations and communities and control ecosystem process. However, we are still in need of synthetic approaches to better understand how positive interactions scale spatio-temporally across a range of taxa and ecosystems. Here, we synthesize two complementary approaches to more rigorously describe positive interactions and their consequences among organisms, across taxa, and over spatio-temporal scales. In the first approach, which we call the mechanistic approach, we make a distinction between two principal mechanisms of facilitation-habitat modification and resource modification. Considering the differences in these two mechanisms is critical because it delineates the potential spatio-temporal bounds over which a positive interaction can occur. We offer guidance on improved sampling regimes for quantification of these mechanistic interactions and their consequences. Second, we present a trait-based approach in which traits of facilitators or traits of beneficiaries can modulate their magnitude of effect or how they respond to either of the positive interaction mechanisms, respectively. Therefore, both approaches can be integrated together by quantifying the degree to which a focal facilitator's or beneficiary's traits explain the magnitude of a positive effect in space and time. Furthermore, we demonstrate how field measurements and analytical techniques can be used to collect and analyze data to test the predictions presented herein. We conclude by discussing how these approaches can be applied to contemporary challenges in ecology, such as conservation and restoration and suggest avenues for future research.

Bivalve Impacts in Freshwater and Marine Ecosystems

Bivalve molluscs are abundant in marine and freshwater ecosystems and perform important ecological functions. Bivalves have epifaunal or infaunal lifestyles but are largely filter feeders that couple the water column and benthos. Bivalve ecology is a large field of study, but few comparisons among aquatic ecosystems or lifestyles have been conducted. Bivalves impact nutrient cycling, create and modify habitat, and affect food webs directly (i.e., prey) and indirectly (i.e., movement of nutrients and energy). Materials accumulated in soft tissue and shells are used as environmental monitors. Freshwater mussel and oyster aggregations in rivers and estuaries are hot spots for biodiversity and biogeochemical transformations. Historically, human use includes food, tools, currency, and ornamentation. Bivalves provide direct benefits to modern cultures as food, building materials, and jewelry and provide indirect benefits by stabilizing shorelines and mitigating nutrient pollution. Research on bivalve-mediated ecological processes is diverse, and future synthesis will require collaboration across conventional disciplinary boundaries.

Prioritizing sites for conservation based on similarity to historical baselines and feasibility of protection

The concept of shifting baselines in conservation science implies advocacy for the use of historical knowledge to inform these baselines but does not address the feasibility of restoring sites to those baselines. In many regions, conservation feasibility varies among sites due to differences in resource availability, statutory power, and land-owner participation. We used zooarchaeological records to identify a historical baseline of the freshwater mussel community's composition before Euro-American influence at a river-reach scale (i.e., a kilometer stretch of river that is abiotically similar) in the Leon River of central Texas (U.S.A.). We evaluated how the community reference position and the feasibility of conservation might enable identification of sites where conservation actions would preserve historically representative communities and be likely to succeed. We devised a conceptual model that incorporated community information and landscape factors to link the best conservation areas to potential cost and conservation benefits. Using fuzzy ordination, we identified modern mussel beds that were most like the historical baseline. We then quantified housing density and land use near each river reach identified to estimate feasibility of habitat restoration. Using our conceptual framework, we identified reaches of high conservation value (i.e., contain the best mussel beds) and where restoration actions would be most likely to succeed. Reaches above Lake Belton were most similar in species composition and relative abundance to zooarchaeological sites. A subset of these mussel beds occurred in locations where conservation actions appeared most feasible. Our results show how to use zooarchaeological data (biodiversity data often readily available) and estimates of conservation feasibility to inform conservation priorities at a local spatial scale.

Environmental DNA (eDNA) Shedding and Decay Rates to Model Freshwater Mussel eDNA Transport in a River

Freshwater mussels are vital components of stream ecosystems, yet remain threatened. Thus, timely and accurate species counts are critical for proper conservation and management. Mussels live in stream sediments and can be challenging to survey given constraints related to water depth, flow, and time of year. The use of environmental DNA (eDNA) to monitor mussel distributions and diversity is a promising tool. Before it can be used as a monitoring tool, however, we need to know how much eDNA mussels shed into their environment and how long the eDNA persists. Here, we present a novel application of eDNA to estimate both the presence/absence and abundance of a freshwater mussel species, Lampsilis siliquoidea. The eDNA shedding and decay rates reported within are the first for freshwater mussels. We determined that eDNA shedding was statistically similar across mussel densities, but that first-order decay constants varied between experimental treatments. Finally, we effectively modeled downstream transport of eDNA and present a model that can be used as a complementary tool to estimate mussel density. Our results suggest that eDNA has the potential to be a complementary tool to survey mussels and enhance current efforts to monitor and protect freshwater mussel biodiversity.

Effect of freshwater mussels on the vertical distribution of anaerobic ammonia oxidizers and other nitrogen-transforming microorganisms in upper Mississippi river sediment

Targeted qPCR and non-targeted amplicon sequencing of 16S rRNA genes within sediment layers identified the anaerobic ammonium oxidation (anammox) niche and characterized microbial community changes attributable to freshwater mussels. Anammox bacteria were normally distributed (Shapiro-Wilk normality test, W-statistic =0.954, p = 0.773) between 1 and 15 cm depth and were increased by a factor of 2.2 (p < 0.001) at 3 cm below the water-sediment interface when mussels were present. Amplicon sequencing of sediment at depths relevant to mussel burrowing (3 and 5 cm) showed that mussel presence reduced observed species richness (p = 0.005), Chao1 diversity (p = 0.005), and Shannon diversity (p < 0.001), with more pronounced decreases at 5 cm depth. A non-metric, multidimensional scaling model showed that intersample microbial species diversity varied as a function of mussel presence, indicating that sediment below mussels harbored distinct microbial communities. Mussel presence corresponded with a 4-fold decrease in a majority of operational taxonomic units (OTUs) classified in the phyla Gemmatimonadetes, Actinobacteria, Acidobacteria, Plantomycetes, Chloroflexi, Firmicutes, Crenarcheota, and Verrucomicrobia. 38 OTUs in the phylum Nitrospirae were differentially abundant (p < 0.001) with mussels, resulting in an overall increase from 25% to 35%. Nitrogen (N)-cycle OTUs significantly impacted by mussels belonged to anammmox genus Candidatus Brocadia, ammonium oxidizing bacteria family Nitrosomonadaceae, ammonium oxidizing archaea genus Candidatus Nitrososphaera, nitrite oxidizing bacteria in genus Nitrospira, and nitrate- and nitrite-dependent anaerobic methane oxidizing organisms in the archaeal family “ANME-2d” and bacterial phylum “NC10”, respectively. Nitrosomonadaceae (0.9-fold (p < 0.001)) increased with mussels, while NC10 (2.1-fold (p < 0.001)), ANME-2d (1.8-fold (p < 0.001)), and Candidatus Nitrososphaera (1.5-fold (p < 0.001)) decreased with mussels. Co-occurrence of 2-fold increases in Candidatus Brocadia and Nitrospira in shallow sediments suggests that mussels may enhance microbial niches at the interface of oxic–anoxic conditions, presumably through biodeposition and burrowing. Furthermore, it is likely that the niches of Candidatus Nitrososphaera and nitrite- and nitrate-dependent anaerobic methane oxidizers were suppressed by mussel biodeposition and sediment aeration, as these phylotypes require low ammonium concentrations and anoxic conditions, respectively. As far as we know, this is the first study to characterize freshwater mussel impacts on microbial diversity and the vertical distribution of N-cycle microorganisms in upper Mississippi river sediment. These findings advance our understanding of ecosystem services provided by mussels and their impact on aquatic biogeochemical N-cycling.

Importance of Riparian Zone: Effects of Resource Availability at Land-water Interface

Riparian zone provides a variety of resources to organisms, including availability of water and subsidies. Water availability in riparian areas influences species distribution and trophic interaction of terrestrial food webs. Cross-ecosystem subsidies as resource flux of additional energy, nutrients, and materials benefit riparian populations and communities (e.g. plants, spiders, lizards, birds and mammals). However, aquatic ecosystems and riparian zones are prone to anthropogenic disturbances, which change water availability and affect the flux dynamics of cross-system subsidies. Yet, we still lack sufficient empirical studies assessing impacts of disturbances of land use, climate change and invasive species individually and interactively on aquatic and riparian ecosystems through influencing subsidy resource availability. In filling this knowledge gap, we can make more effective efforts to protect and conserve riparian habitats and biodiversity, and maintain riparian ecosystem functioning and services.

Resource subsidies between stream and terrestrial ecosystems under global change

Streams and adjacent terrestrial ecosystems are characterized by permeable boundaries that are crossed by resource subsidies. Although the importance of these subsidies for riverine ecosystems is increasingly recognized, little is known about how they may be influenced by global environmental change. Drawing from available evidence, in this review we propose a conceptual framework to evaluate the effects of global change on the quality and spatiotemporal dynamics of stream-terrestrial subsidies. We illustrate how changes to hydrological and temperature regimes, atmospheric CO2 concentration, land use and the distribution of nonindigenous species can influence subsidy fluxes by affecting the biology and ecology of donor and recipient systems and the physical characteristics of stream-riparian boundaries. Climate-driven changes in the physiology and phenology of organisms with complex life cycles will influence their development time, body size and emergence patterns, with consequences for adjacent terrestrial consumers. Also, novel species interactions can modify subsidy dynamics via complex bottom-up and top-down effects. Given the seasonality and pulsed nature of subsidies, alterations of the temporal and spatial synchrony of resource availability to consumers across ecosystems are likely to result in ecological mismatches that can scale up from individual responses, to communities, to ecosystems. Similarly, altered hydrology, temperature, CO2 concentration and land use will modify the recruitment and quality of riparian vegetation, the timing of leaf abscission and the establishment of invasive riparian species. Along with morphological changes to stream-terrestrial boundaries, these will alter the use and fluxes of allochthonous subsidies associated with stream ecosystems. Future research should aim to understand how subsidy dynamics will be affected by key drivers of global change, including agricultural intensification, increasing water use and biotic homogenization. Our conceptual framework based on the match-mismatch between donor and recipient organisms may facilitate understanding of the multiple effects of global change and aid in the development of future research questions.

A Global Analysis of the Relationship between Farmed Seaweed Production and Herbivorous Fish Catch

Globally, farmed seaweed production is expanding rapidly in shallow marine habitats. While seaweed farming provides vital income to millions of artisanal farmers, it can negatively impact shallow coral reef and seagrass habitats. However, seaweed farming may also potentially provide food subsidies for herbivorous reef fish such as the Siganidae, a valuable target family, resulting in increased catch. Comparisons of reef fish landings across the central Philippines revealed that the catch of siganids was positively correlated to farmed seaweed production whilst negatively correlated to total reef fish catch over the same period of time. We tested the generality of this pattern by analysing seaweed production, siganid catch, and reef fish catch for six major seaweed-producing countries in the tropics. We hypothesized that increased seaweed production would correspond with increased catch of siganids but not other reef fish species. Analysis of the global data showed a positive correlation between farmed seaweeds and siganids in Southeast Asia (Indonesia, Malaysia, and the Philippines) but not Africa (Tanzania and Zanzibar), or the Western Pacific (Fiji). In Southeast Asia, siganid catch increased disproportionately faster with seaweed production than did reef fish catch. Low continuity, sporadic production and smaller volumes of seaweed farming may explain the differences.

Drought-induced changes in flow regimes lead to long-term losses in mussel-provided ecosystem services

Extreme hydro-meteorological events such as droughts are becoming more frequent, intense, and persistent. This is particularly true in the south central USA, where rapidly growing urban areas are running out of water and human-engineered water storage and management are leading to broad-scale changes in flow regimes. The Kiamichi River in southeastern Oklahoma, USA, has high fish and freshwater mussel biodiversity. However, water from this rural river is desired by multiple urban areas and other entities. Freshwater mussels are large, long-lived filter feeders that provide important ecosystem services. We ask how observed changes in mussel biomass and community composition resulting from drought-induced changes in flow regimes might lead to changes in river ecosystem services. We sampled mussel communities in this river over a 20-year period that included two severe droughts. We then used laboratory-derived physiological rates and river-wide estimates of species-specific mussel biomass to estimate three aggregate ecosystem services provided by mussels over this time period: biofiltration, nutrient recycling (nitrogen and phosphorus), and nutrient storage (nitrogen, phosphorus, and carbon). Mussel populations declined over 60%, and declines were directly linked to drought-induced changes in flow regimes. All ecosystem services declined over time and mirrored biomass losses. Mussel declines were exacerbated by human water management, which has increased the magnitude and frequency of hydrologic drought in downstream reaches of the river. Freshwater mussels are globally imperiled and declining around the world. Summed across multiple streams and rivers, mussel losses similar to those we document here could have considerable consequences for downstream water quality although lost biofiltration and nutrient retention. While we cannot control the frequency and severity of climatological droughts, water releases from reservoirs could be used to augment stream flows and prevent compounded anthropogenic stressors.

A tale of two rivers: implications of water management practices for mussel biodiversity outcomes during droughts

Droughts often pose situations where stream water levels are lowest while human demand for water is highest. Here we present results of an observational study documenting changes in freshwater mussel communities in two southern US rivers during a multi-year drought. During a 13-year period water releases into the Kiamichi River from an impoundment were halted during droughts, while minimum releases from an impoundment were maintained in the Little River. The Kiamichi observed nearly twice as many low-flow events known to cause mussel mortality than the Little, and regression tree analyses suggest that this difference was influenced by reduced releases. During this period mussel communities in the Kiamichi declined in species richness and abundance, changes that were not observed in the Little. These results suggest that reduced releases during droughts likely led to mussel declines in one river, while maintaining reservoir releases may have sustained mussel populations in another.