Anthony A. Chariton

Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA

Biodiversity assessment underpins our understanding of ecosystems and determines environmental management decisions on resource use and conservation priorities. Recently, a new discipline – environmental or ecological genomics (ecogenomics) – has emerged from major advances in sequencing technologies, such as pyrosequencing (a technique based on the detection of pyrophosphate during nucleotide incorporation), and enabled extraordinary progress in the way biodiversity can be assessed. Since 2008, numerous high-impact microbial metagenomic sequencing studies, which have relied on both classical and next-generation sequencing, have been published. As a result, many previously unrecognized taxa and biota have been identified, but none of these studies explored eukaryote diversity. Here, we illustrate the power of applying next-generation pyrosequencing to identify and enumerate eukaryote species assemblages in the context of assessing the impacts of human activity on ecosystems.

Impacts of inundation and drought on eukaryote biodiversity in semi-arid floodplain soils

Floodplain ecosystems are characterized by alternating wet and dry phases and periodic inundation defines their ecological character. Climate change, river regulation and the construction of levees have substantially altered natural flooding and drying regimes worldwide with uncertain effects on key biotic groups. In southern Australia, we hypothesized that soil eukaryotic communities in climate change affected areas of a semi‐arid floodplain would transition towards comprising mainly dry‐soil specialist species with increasing drought severity. Here, we used 18S rRNA amplicon pyrosequencing to measure the eukaryote community composition in soils that had been depleted of water to varying degrees to confirm that reproducible transitional changes occur in eukaryotic biodiversity on this floodplain. Interflood community structures (3 years post‐flood) were dominated by persistent rather than either aquatic or dry‐specialist organisms. Only 2% of taxa were unique to dry locations by 8 years post‐flood, and 10% were restricted to wet locations (inundated a year to 2 weeks post‐flood). Almost half (48%) of the total soil biota were detected in both these environments. The discovery of a large suite of organisms able to survive nearly a decade of drought, and up to a year submerged supports the concept of inherent resilience of Australian semi‐arid floodplain soil communities under increasing pressure from climatic induced changes in water availability.

Metabarcoding of benthic eukaryote communities predicts the ecological condition of estuaries

DNA-derived measurements of biological composition have the potential to produce data covering all of life, and provide a tantalizing proposition for researchers and managers. We used metabarcoding to compare benthic eukaryote composition from five estuaries of varying condition. In contrast to traditional studies, we found biotic richness was greatest in the most disturbed estuary, with this being due to the large volume of extraneous material (i.e. run-off from aquaculture, agriculture and other catchment activities) being deposited in the system. In addition, we found strong correlations between composition and a number of environmental variables, including nutrients, pH and turbidity. A wide range of taxa responded to these environmental gradients, providing new insights into their sensitivities to natural and anthropogenic stressors. Metabarcoding has the capacity to bolster current monitoring techniques, enabling the decisions regarding ecological condition to be based on a more holistic view of biodiversity.

Influence of the choice of physical and chemistry variables on interpreting patterns of sediment contaminants and their relationships with estuarine macrobenthic communities

A primary objective of contaminated sediment risk assessments is to identify if contaminant enrichment is eliciting an ecological response. Using complementary environmental and biotic datasets, we examined five scenarios with respect to: dataset complexity; metal extraction; normalisation of organics; the inclusion/exclusion of acid-volatile sulfide data, and iron and manganese concentrations. Spatial distributions of abiotic variables were examined by principal components analysis, with canonical correspondence analysis used to examine the total and partitioning of biological variation. Metals were the dominant contaminant and explained the largest proportion of variation in the macrobenthic data. Extraction procedure and carbon normalisation of organics had little influence on the overall analysis. Porewater metal data was essential for interpretation, with excess of acid-volatile sulfide over simultaneously extractable metals being a poor surrogate. In the canonical correspondence analyses, the inclusion of Fe/Mn accentuated the covariation between the ecological and contaminant variables. Multimodel comparisons aided interpretation by emphasising specific relationships among environmental variables and their interactions with the biotic data. Furthermore, for future examinations of the described system, the findings can be used to reduce the collection of redundant environmental variables or variables that are poorly correlated with changes in macrobenthic assemblages.

Improved Inference of Taxonomic Richness from Environmental DNA

Accurate estimation of biological diversity in environmental DNA samples using high-throughput amplicon pyrosequencing must account for errors generated by PCR and sequencing. We describe a novel approach to distinguish the underlying sequence diversity in environmental DNA samples from errors that uses information on the abundance distribution of similar sequences across independent samples, as well as the frequency and diversity of sequences within individual samples. We have further refined this approach into a bioinformatics pipeline, Amplicon Pyrosequence Denoising Program (APDP) that is able to process raw sequence datasets into a set of validated sequences in formats compatible with commonly used downstream analyses packages. We demonstrate, by sequencing complex environmental samples and mock communities, that APDP is effective for removing errors from deeply sequenced datasets comprising biological and technical replicates, and can efficiently denoise single-sample datasets. APDP provides more conservative diversity estimates for complex datasets than other approaches; however, for some applications this may provide a more accurate and appropriate level of resolution, and result in greater confidence that returned sequences reflect the diversity of the underlying sample.

Arsenic distribution and species in two Zostera capricorni seagrass ecosystems, New South Wales, Australia

Arsenic concentrations and species were compared in biota from two Zostera capricorni ecosystems. Mean arsenic concentrations were not significantly different for non-vegetative sediment, rhizosphere sediment, Z. capricorni blades, roots, rhizomes, epiphytes, amphipods, polychaetes, molluscs, crustaceans and fish, but were significantly different in detritus. Sediments and plant tissues contained mostly inorganic arsenic and PO4-arsenoriboside. Detritus contained mostly PO4-arsenoriboside. Fish tissues contained predominately arsenobetaine. Other animals had lower proportions of arsenobetaine and variable quantities of minor arsenic species. Bioconcentration but not biomagnification ofarsenicisoccurringwithnoevidenceofarsenichyperaccumulation.Theproportionofarsenobetaineincreasesthrough the food web and is attributed to a shift from a mixed diet at lower trophic levels to animals containing mostly arsenobetaineathighertrophiclevelsandthemoreefficientretentionofarsenobetaine,comparedtootherarsenic species.

A Classification of Floodplains and Wetlands of the Murray-Darling Basin Based on Changes in Flows Following Water Resource Development

We present a regional classification of 40 floodplains and wetlands of the Murray-Darling Basin, Australia, based on changes in flows since river regulation and water resource development. The classification is based on a similarity percentage analysis of nine metrics relating to frequency, duration and volume of floods, and seasonality of flows. The major changes in flows were a delay in mean Julian day of occurrence of low flow and reduced variation in occurrence, lower frequency of flood events and reduced variation of flood duration. The spatial distribution of floodplain classes highlights the differential effects of river regulation across the Basin, with greatest change in rivers in the southern Basin, particularly the Murray, Murrumbidgee, and Lachlan, and the least change in unregulated or less-regulated rivers, predominantly in the north. There is generally good spatial concordance between distribution of floodplain classes and the Murray-Darling Basin Sustainable Rivers Audit index of riverine ecosystem health, and the distribution of major communities of waterbirds. Our results suggest, when compared with published reports of ecological condition, that very low-gradient, terminal floodplain wetlands characterized by low discharge volume and anastomosing distributary channels may be particularly susceptible to adverse ecological impacts arising from relatively slight alterations to flows.

Emergent technologies and analytical approaches for understanding the effects of multiple stressors in aquatic environments

In order to assess how emerging science and new tools can be applied to study multiple stressors on a large (ecosystem) scale and to facilitate greater integration of approaches among different scientific disciplines, a workshop was held on 10–12 September 2014 at the Sydney Institute of Marine Sciences, Sydney, Australia. This workshop aimed to explore the potential offered by new approaches to characterise stressor regimes, to explore stressor-response relationships among biota, to design better early-warning systems and to develop smart tools to support sustainable management of human activities, through more efficient regulation. In this paper we highlight the key issues regarding biological coverage, the complexity of multiply stressed environments, and our inability to predict the biological effects under such scenarios. To address these challenges, we provide an extension of the current Environmental Risk Assessment framework. Underpinning this extension is the harnessing of environmental-genomic data, which has the capacity to provide a broader view of diversity, and to express the ramifications of multiple stressors across multiple levels of biological organisation. We continue to consider how these and other emerging data sources may be combined and analysed using new statistical approaches for disentangling the effects of multiple stressors.

Faster, Higher and Stronger? The Pros and Cons of Molecular Faunal Data for Assessing Ecosystem Condition

Abstract Ecological observation of global change processes is dependent on matching the scale and quality of biological data with associated geophysical and geochemical driver information. Until recently, the scale and quality of biological observation on natural assemblages has often failed to match data generated through physical or chemical platforms due to constraints of cost and taxonomic resolution. With the advent of next-generation DNA sequencing platforms, creating ‘big data’ scale observations of biological assemblages across a wide range of phylogenetic groups are now a reality. Here we draw from a variety of studies to illustrate the potential benefits and drawbacks of this new data source for enhancing our observation of ecological change compared with traditional methods. We focus on a key habitat—estuaries—which are among the most threatened by anthropogenic change processes. When community composition data derived using morphological and molecular approaches were compared, the increased level of taxonomic resolution from the molecular approach allowed for greater discrimination between estuaries. Apart from higher taxonomic resolution, there was also an order of magnitude more taxonomic units recorded in the molecular approach relative to the morphological. While the morphological data set was constrained to traditional macroinvertebrate sampling, the molecular tools could be used to sample a wide range of taxa from the microphytobenthos, e.g., diatoms and dinoflagellates. Furthermore, the information provided by molecular techniques appeared to be more sensitive to a range of well-established drivers of benthic ecology. Our results indicated that molecular approaches are now sufficiently advanced to provide not just equivalent information to that collected using traditional morphological approaches, but rather an order of magnitude bigger, better, and faster data with which to address pressing ecological questions.

Spatial variability of cadmium, copper, manganese, nickel and zinc in the Port Curtis Estuary, Queensland, Australia

Port Curtis is a rapidly growing industrialised and urbanised harbour in Central Queensland, Australia. The spatial variability of trace metals in waters and suspended particulates was determined along axial transects within the harbour and in oceanic waters adjacent to Port Curtis. Dissolved metal concentrations were significantly elevated in Port Curtis compared with the concentrations measured in the adjacent coastal waters. Dissolved copper and zinc concentrations ranged from <19 to 800 and <31 to 580 ng L −1 , respectively, and maxima were observed in inner harbour waters adjacent to the southern entrance to the Narrows and in close proximity to anthropogenic sources. Dissolved nickel concentrations were measured in the range of 110 to 900 ng L −1 , and exhibited a maximum concentration in the central to northern Narrows, in an area that was not adjacent to anthropogenic sources. Dissolved manganese concentration maxima were measured in close proximity to the dissolved nickel maxima. It appears likely that the elevated dissolved metal concentrations in Port Curtis and the Narrows were not caused by a single point source, and are the result of several factors, including industrial activity around the foreshore, fluxes from sediment-porewater, low flushing durations, lower water pH and possibly episodic inputs from adjacent rivers.