Soil and Freshwater and Marine Sediment Food Webs: Their Structure and Function

Nematodes alter the taxonomic and functional profiles of benthic bacterial communities: A metatranscriptomic approach

Marine sediments cover 70% of the Earth's surface, and harbour diverse bacterial communities critical for marine biogeochemical processes, which affect climate change, biodiversity and ecosystem functioning. Nematodes, the most abundant and species-rich metazoan organisms in marine sediments, in turn, affect benthic bacterial communities and bacterial-mediated ecological processes, but the underlying mechanisms by which they affect biogeochemical cycles remain poorly understood. Here, we demonstrate using a metatranscriptomic approach that nematodes alter the taxonomic and functional profiles of benthic bacterial communities. We found particularly strong stimulation of nitrogen-fixing and methane-oxidizing bacteria in the presence of nematodes, as well as increased functional activity associated with methane metabolism and degradation of various carbon compounds. This study provides empirical evidence that the presence of nematodes results in taxonomic and functional shifts in active bacterial communities, indicating that nematodes may play an important role in benthic ecosystem processes.

Compound-specific stable isotope analysis of amino acid nitrogen reveals detrital support of microphytobenthos in the Dutch Wadden Sea benthic food web

The Wadden Sea is the world’s largest intertidal ecosystem and provides vital food resources for a large number of migratory bird and fish species during seasonal stopovers. Previous work using bulk stable isotope analysis of carbon found that microphytobenthos (MPB) was the dominant resource fueling the food web with particulate organic matter making up the remainder. However, this work was unable to account for the trophic structure of the food web or the considerable increase in δ15N values of bulk tissue throughout the benthic food web occurring in the Eastern regions of the Dutch Wadden Sea. Here, we combine compound-specific and bulk analytical stable isotope techniques to further resolve the trophic structure and resource use throughout the benthic food web in the Wadden Sea. Analysis of δ15N for trophic and source amino acids allowed for better identification of trophic relationships due to the integration of underlying variation in the nitrogen resources supporting the food web. Baseline-integrated trophic position estimates using glutamic acid (Glu) and phenylalanine (Phe) allow for disentanglement of baseline variations in underlying δ15N sources supporting the ecosystem and trophic shifts resulting from changes in ecological relationships. Through this application, we further confirmed the dominant ecosystem support by MPB-derived resources, although to a lesser extent than previously estimated. In addition to phytoplankton-derived particulate, organic matter and MPB supported from nutrients from the overlying water column there appears to be an additional resource supporting the benthic community. From the stable isotope mixing models, a subset of species appears to focus on MPB supported off recycled (porewater) N and/or detrital organic matter mainly driven by increased phenylalanine δ15N values. This additional resource within MPB may play a role in subsidizing the exceptional benthic productivity observed within the Wadden Sea ecosystem and reflect division in MPB support along green (herbivory) and brown (recycled/detrital) food web pathways.

Network analysis reveals microbe-mediated impacts of aeration on deep sediment layer microbial communities

Over-aeration is a common remediation strategy for black and odorous water bodies, in which oxygen is introduced to impact aquatic microbial communities as an electron acceptor of high redox potential. In this study, black-odorous freshwater sediments were cultured for 9 weeks under aeration to investigate microbial covariations at different depths and time points. Based on community 16S rRNA gene sequencing, the microbial covariations were visualized using phylogenetic microbial ecological networks (pMENs). In the spatial scale, we identified smaller and more compact pMENs across all layers compared with the anaerobic control sediments, in terms of network size, average node connectivity, and modularity. The aerated middle layer had the most connectors, the least module hubs, a network hub, shorter average path length, and predominantly positive covariations. In addition, a significant sulfate accumulation in the aerated middle layer indicated the most intense sulfide oxidation, possibly because aeration prompted sediment surface Desulfobulbaceae, known as cable bacteria, to reach the middle layer. In the time scale, similarly, aeration led to smaller pMEN sizes and higher portions of positive covariations. Therefore, we conclude that elevated dissolved oxygen at the water-sediment interface may impact not only the surface sediment but also the subsurface and/or deep sediment microbial communities mediated by microorganisms, particularly by Desulfobulbaceae.

The functional role and diversity of soil nematodes are stronger at high elevation in the lesser Himalayan Mountain ranges

Soil nematodes are a foremost component of terrestrial biodiversity; they display a whole gamut of trophic guilds and life strategies, and by their activity, affect major ecosystem process, such as organic matter degradation and carbon cycling. Based on nematodes' functional types, nematode community indices have been developed, and can be used to link variation in nematodes community composition and ecosystem processes. Yet, the use of these indices has been mainly restricted to anthropogenic stresses. In this study, we propose to expand the use of nematodes' derived ecological indices to link soil and climate properties with soil food webs, and ecosystem processes that all vary along steep elevation gradients. For this purpose, we explored how elevation affects the trophic and functional diversity of nematode communities sampled every 300 m, from about 1,000 m to 3,700 m above sea level, across four transects in the lesser Himalayan range of Jammu and Kashmir. We found that (a) the trophic and functional diversity of nematodes increases with elevation; (b) differences in nematodes communities generate habitat-specific functional diversity; (c) the maturity index (ΣMI) increases with elevation, while the enrichment index decreases, indicating less mature and less productive ecosystems, enhanced fungal-based energy flow, and a predominant role of nematodes in generating carbon influxes at high-elevation sites. We thus confirm that the functional contribution of soil nematodes to belowground ecosystem processes, including carbon and energy flow, is stronger at high elevation. Overall, this study highlights the central importance of nematodes in sustaining soil ecosystems and brings insights into their functional role, particularly in alpine and arctic soils.

Role of Biofilms in Contaminant Bioaccumulation and Trophic Transfer in Aquatic Ecosystems: Current State of Knowledge and Future Challenges

In freshwater environments, microbial assemblages attached to submerged substrates play an essential role in ecosystem processes such as primary production, supported by periphyton, or organic matter decomposition, supported by microbial communities attached to leaf litter or sediments. These microbial assemblages, also called biofilms, are not only involved in nutrients fluxes but also in contaminants dynamics. Biofilms can accumulate metals and organic contaminants transported by the water flow and/or adsorbed onto substrates. Furthermore, due to their high metabolic activity and their role in aquatic food webs, microbial biofilms are also likely to influence contaminant fate in aquatic ecosystems. In this review, we provide (1) a critical overview of the analytical methods currently in use for detecting and quantifying metals and organic micropollutants in microbial biofilms attached to benthic substrata (rocks, sediments, leaf litter); (2) a review of the distribution of those contaminants within aquatic biofilms and the role of these benthic microbial communities in contaminant fate; (3) a set of future challenges concerning the role of biofilms in contaminant accumulation and trophic transfers in the aquatic food web. This literature review highlighted that most knowledge on the interaction between biofilm and contaminants is focused on contaminants dynamics in periphyton while technical limitations are still preventing a thorough estimation of contaminants accumulation in biofilms attached to leaf litter or sediments. In addition, microbial biofilms represent an important food resource in freshwater ecosystems, yet their role in dietary contaminant exposure has been neglected for a long time, and the importance of biofilms in trophic transfer of contaminants is still understudied.

Trophic structure of the macrofauna associated to deep-vents of the southern Gulf of California: Pescadero Basin and Pescadero Transform Fault

Newly discovered hydrothermal systems in the Pescadero Basin (PB) and the neighboring Pescadero Transform Fault (PTF) at the mouth of the Gulf of California disclosed a diverse macrofauna assemblage. The trophic structure of both ecosystems was assessed using carbon (δ¹³C), nitrogen (δ¹⁵N), and sulfur (δ³⁴S) stable isotopes. The δ¹³C ranged from -40.8 to -12.1‰, revealing diverse carbon sources and its assimilation via Calvin-Benson-Bassham and the reductive tricarboxylic acid cycles. The δ¹⁵N values were between -12.5 and 18.3‰, corresponding to primary and secondary consumers. The δ³⁴S values fluctuated from -36.2 to 15.1‰, indicating the sulfide assimilation of biogenic, magmatic, and photosynthetic sources. In PB high-temperature vents, primary consumers including symbiont-bearing, bacterivores and filter-feeders predominated. The secondary consumers within the scavengers/detritivores and predator guilds were scarce. The siboglinid Oasisia aff alvinae dominated the macrofauna assemblage at PB, but rather than playing a trophic role, it provides a substrate to vent dwellers. In PTF low-temperature vents, only symbiont-bearing primary consumers were analyzed, displaying the lowest δ³⁴S values. This assemblage was dominated by the coexisting siboglinids Lamellibrachia barhami and Escarpia spicata. δ³⁴S values allowed to distinguish between PB and PTF vent communities, to exclude the presence of methanotrophic organisms, and the detection of photosynthetic organic matter input.

A Worm's World: Ecological Flexibility Pays Off for Free-Living Nematodes in Sediments and Soils

Free-living nematodes, an ancient animal phylum of unsegmented microscopic roundworms, have successfully adapted to nearly every ecosystem on Earth: from marine and freshwater to land, from the polar regions to the tropics, and from the mountains to the ocean depths. They are globally the most abundant animals in sediments and soils. In the present article, we identify the factors that collectively explain the successful ecological proliferation of free-living nematodes and demonstrate the impact they have on vital sediment and soil processes. The ecological success of nematodes is strongly linked to their ability to feed on various food sources that are present in both sediments and soils, and to proliferate rapidly and survive in contrasting environmental conditions. The adaptations, roles, and behaviors of free-living nematodes have important implications for the resilience of sediments and soils, and for emergent animal communities responding to human alterations to ecosystems worldwide.

Insights from the Genomes of Microbes Thriving in Uranium-Enriched Sediments

Elevated uranium dose (4 g kg^-1) causes a shift in billabong sediment communities that result in the enrichment of five bacterial species. These taxa include Geobacter, Geothrix and Dyella species, as well as a novel-potentially predatory-Bacteroidetes species, and a new member of class Anaerolineae (Chloroflexi). Additionally, a population of methanogenic Methanocella species was also identified. Genomic reconstruction and metabolic examination of these taxa reveal a host of divergent life strategies and putative niche partitioning. Resistance-nodulation-division heavy metal efflux (RND-HME) transporters are implicated as potential uranium tolerance strategies among the bacterial taxa. Potential interactions, uranium tolerance and ecologically relevant catabolism are presented in a conceptual model of life in this environment.

Tracing the Enterococci from Paleozoic Origins to the Hospital

We examined the evolutionary history of leading multidrug resistant hospital pathogens, the enterococci, to their origin hundreds of millions of years ago. Our goal was to understand why, among the vast diversity of gut flora, enterococci are so well adapted to the modern hospital environment. Molecular clock estimation, together with analysis of their environmental distribution, phenotypic diversity, and concordance with host fossil records, place the origins of the enterococci around the time of animal terrestrialization, 425-500 mya. Speciation appears to parallel the diversification of hosts, including the rapid emergence of new enterococcal species following the End Permian Extinction. Major drivers of speciation include changing carbohydrate availability in the host gut. Life on land would have selected for the precise traits that now allow pathogenic enterococci to survive desiccation, starvation, and disinfection in the modern hospital, foreordaining their emergence as leading hospital pathogens.

Global change impacts on river ecosystems: A high-resolution watershed study of Ebro river metabolism

Global change is transforming freshwater ecosystems, mainly through changes in basin flow dynamics. This study assessed how the combination of climate change and human management of river flow impacts metabolism of the Ebro River (the largest river basin in Spain, 86,100km(2)), assessed as gross primary production-GPP-and ecosystem respiration-ER. In order to investigate the influence of global change on freshwater ecosystems, an analysis of trends and frequencies from 25 sampling sites of the Ebro river basin was conducted. For this purpose, we examined the effect of anthropogenic flow control on river metabolism with a Granger causality study; simultaneously, took into account the effects of climate change, a period of extraordinary drought (largest in past 140years). We identified periods of sudden flow changes resulting from both human management and global climate effects. From 1998 to 2012, the Ebro River basin was trending toward a more autotrophic condition indicated by P/R ratio. Particularly, the results show that floods that occurred after long periods of low flows had a dramatic impact on the respiration (i.e., mineralization) capacity of the river. This approach allowed for a detailed characterization of the relationships between river metabolism and drought impacts at the watershed level. These findings may allow for a better understanding of the ecological impacts provoked by flow management, thus contributing to maintain the health of freshwater communities and ecosystem services that rely on their integrity.

The significance of linoleic acid in food sources for detritivorous benthic invertebrates

Chemical composition of organic matter (OM) is a key driver for detritus consumption by macroinvertebrates and polyunsaturated fatty acid (PUFA) content is considered a candidate indicator of food palatability. Since traditionally used complex natural OM covaries in many quality attributes, it remains uncertain whether benthic invertebrates developed an actual preference for PUFA-rich food. Therefore we aimed to test the influence of the PUFA linoleic acid on OM consumption by aquatic macroinvertebrates using standardized surrogate substrates (decomposition and consumption tablet, DECOTAB) with added linoleic acid (PUFA) in comparison to consumption of DECOTAB containing only cellulose (Standard) or ground macrophytes (Plant). In microcosms, we observed a higher consumption rate of PUFA DECOTAB in comparison to Standard DECOTAB in two functionally distinct invertebrate species (Lumbriculus variegatus and Asellus aquaticus). This effect appeared to be overruled in the field due to unknown sources of natural variation. Although we observed higher consumption rates in species-rich ditches compared to species-poor ditches, consumption rates were comparable for all three types of DECOTAB deployed. Upon reduced food quality and palatability, results presented here hint that PUFA like linoleic acid may be a key OM attribute driving the performance of benthic macroinvertebrates and inherent functioning of aquatic ecosystems.

Food web of a confined and anthropogenically affected coastal basin (the Mar Piccolo of Taranto) revealed by carbon and nitrogen stable isotopes analyses

Carbon and nitrogen stable isotope analysis was used to examine the food web of the Mar Piccolo of Taranto, a coastal basin experiencing several anthropogenic impacts. Main food sources (algal detritus, seaweeds, particulate organic matter (POM) and sediment organic matter (SOM)) and benthic and pelagic consumers were collected during two contrasting seasons (June and April), at four sites distributed over two inlets, and characterized by different level of confinements, anthropogenic inputs and the presence of mussels farming. δ(13)C values of organic sources revealed an important contribution of POM to both planktonic and benthic pathways, as well as the influence of terrigenous inputs within both inlets, probably due to high seasonal land runoff. Although δ(13)C of both sources and consumers varied little between sampling sites and dates, δ(15)N spatial variability was higher and clearly reflected the organic enrichment in the second inlet as well as the uptake of anthropogenically derived material by benthic consumers. On the other hand, within the first inlet, the isotopic composition of consumers did not change in response to chemical contamination. However, the impact of polluted sediments near the Navy Arsenal in the first inlet was detectable at the level of the macrobenthic trophic structure, showing high dominance of motile, upper level consumers capable to face transient conditions and the reduction of the more resident deposit feeders. We therefore underline the great potential of matching stable isotope analysis with quantitative studies of community structure to assess the effects of multiple anthropogenic stressors.

Molecular Assessment of Bacterial Community Dynamics and Functional End Points during Sediment Bioaccumulation Tests

Whole sediment toxicity tests play an important role in environmental risk assessment of organic chemicals. It is not clear, however, to what extent changing microbial community composition and associated functions affect sediment test results. We assessed the development of bacterial communities in artificial sediment during a 28 day bioaccumulation test with polychlorinated biphenyls, chlorpyrifos, and four marine benthic invertebrates. DGGE and 454-pyrosequencing of PCR-amplified 16S rRNA genes were used to characterize bacterial community composition. Abundance of total bacteria and selected genes encoding enzymes involved in important microbially mediated ecosystem functions were measured by qPCR. Community composition and diversity responded most to the time course of the experiment, whereas organic matter (OM) content showed a low but significant effect on community composition, biodiversity and two functional genes tested. Moreover, OM content had a higher influence on bacterial community composition than invertebrate species. Medium OM content led to the highest gene abundance and is preferred for standard testing. Our results also indicated that a pre-equilibration period is essential for growth and stabilization of the bacterial community. The observed changes in microbial community composition and functional gene abundance may imply actual changes in such functions during tests, with consequences for exposure and toxicity assessment.

Herbivory and Stoichiometric Feedbacks to Primary Production

Established theory addresses the idea that herbivory can have positive feedbacks on nutrient flow to plants. Positive feedbacks likely emerge from a greater availability of organic carbon that primes the soil by supporting nutrient turnover through consumer and especially microbially-mediated metabolism in the detrital pool. We developed an entirely novel stoichiometric model that demonstrates the mechanism of a positive feedback. In particular, we show that sloppy or partial feeding by herbivores increases detrital carbon and nitrogen allowing for greater nitrogen mineralization and nutritive feedback to plants. The model consists of differential equations coupling flows among pools of: plants, herbivores, detrital carbon and nitrogen, and inorganic nitrogen. We test the effects of different levels of herbivore grazing completion and of the stoichiometric quality (carbon to nitrogen ratio, C:N) of the host plant. Our model analyses show that partial feeding and plant C:N interact because when herbivores are sloppy and plant biomass is diverted to the detrital pool, more mineral nitrogen is available to plants because of the stoichiometric difference between the organisms in the detrital pool and the herbivore. This model helps to identify how herbivory may feedback positively on primary production, and it mechanistically connects direct and indirect feedbacks from soil to plant production.

Relating sediment impacts on coral reefs to watershed sources, processes and management: a review

Modification of terrestrial sediment fluxes can result in increased sedimentation and turbidity in receiving waters, with detrimental impacts on coral reef ecosystems. Preventing anthropogenic sediment reaching coral reefs requires a better understanding of the specific characteristics, sources and processes generating the anthropogenic sediment, so that effective watershed management strategies can be implemented. Here, we review and synthesise research on measured runoff, sediment erosion and sediment delivery from watersheds to near-shore marine areas, with a strong focus on the Burdekin watershed in the Great Barrier Reef region, Australia. We first investigate the characteristics of sediment that pose the greatest risk to coral reef ecosystems. Next we track this sediment back from the marine system into the watershed to determine the storage zones, source areas and processes responsible for sediment generation and run-off. The review determined that only a small proportion of the sediment that has been eroded from the watershed makes it to the mid and outer reefs. The sediment transported >1 km offshore is generally the clay to fine silt (<4-16 μm) fraction, yet there is considerable potential for other terrestrially derived sediment fractions (<63 μm) to be stored in the near-shore zone and remobilised during wind and tide driven re-suspension. The specific source of the fine clay sediments is still under investigation; however, the Bowen, Upper Burdekin and Lower Burdekin sub-watersheds appear to be the dominant source of the clay and fine silt fractions. Sub-surface erosion is the dominant process responsible for the fine sediment exported from these watersheds in recent times, although further work on the particle size of this material is required. Maintaining average minimum ground cover >75% will likely be required to reduce runoff and prevent sub-soil erosion; however, it is not known whether ground cover management alone will reduce sediment supply to ecologically acceptable levels.