Rod Oliver

Ecosystem science: toward a new paradigm for managing Australia's inland aquatic ecosystems.

Freshwater ecosystems are a foundation of our social, cultural, spiritual and economic well being. The degraded condition of many of Australias river ecosystems is testament to our failure to manage these resources wisely. Ecosystem science involves the holistic study of complex biophysical systems to understand the drivers that influence ecological pattern and process. Ecosystem science should underpin both water management and policy. Our understanding of aquatic ecosystems lags behind the increasing problems caused by past land and water management. Current post-graduate training programmes will not provide the aquatic ecosystem scientists needed by government and management agencies to prevent further degradation. We advocate new initiatives to capture the skills, knowledge and innovation of our research community by engaging scientists and managers in large-scale, long-term ecosystem science programmes across Australia and to integrate these programmes with community aspirations, policy, planning and management. We call on management agencies to increase their support for and uptake and use of ecosystem science. We also advocate establishment of national archives for long-term ecologically-relevant data and samples, and clear custodial arrangements to protect, update and facilitate knowledge-transfer. These initiatives need to be supported by more extensive, better-funded post-graduate and post-doctoral programmes in ecosystem science and management.

Geochemistry of suspended particulate matter (SPM) in the Murray-Darling River System : A conceptual isotopic/geochemical model for the fractionation of major, trace and rare earth elements

A conceptual isotopic/geochemical model is presented to explain the variation of major, trace and rare earth element (REE) geochemistry and Sr isotope systematics in suspended particulate matter (SPM) as a function of particle/colloid size. This conceptual model is an extension of a previous investigation of the origin of SPM in the Murray-Darling River system (MDRS) that utilised Sr isotope systematics to examine aspects of SPM (particle/colloid) origin, structure and mineralogy. The geochemical processes that give rise to the often coherent trends in major, trace and REE geochemistry and Sr isotopic signature as a function of particulate (<1 μm) and colloidal (>1 μm) size in the MDRS have been identified using an enhanced SPM size fractionation technique as a basis to not only obtain a broad range of particle/colloid size ranges, but also to provide sufficient material for subsequent geochemical and isotopic analysis. The conceptual isotopic/geochemical model proposed here contains three major components: (i) the differential weathering of micas and alkali (K-) feldspars to form the majority of the particulate (<1 μm) fractions (high 87Sr/86Sr ratio), which have a geochemical and Sr isotopic signature that closely resembles precursor mineralogies, (ii) the differential weathering of Na, Ca-feldspars (plagioclase) which decompose to form clay minerals in the colloidal (>1 μm) fractions (low 87Sr/86Sr ratio), with a range of geochemical signatures related to the relative proportions of inorganic and organic constituents, and (iii) the presence of natural organic matter as coatings on the particulate (<1 μm) and colloidal (>1 μm) matter and possibly as organo-colloids which exert an increasing influence in particular on bulk colloid geochemistry with decreasing colloid size. This conceptual isotopic/geochemical model also accounts for the distinct variation in major, trace and REE geochemistry and Sr isotopic systematics between the particulate (<1 μm) and colloidal (>1 μm) fractions, the variation being primarily a function of the distinctly different precursor mineralogies of the SPM fractions and geochemical fractionation during the weathering and transport. Additionally, this model explains a systematic fractionation of REE apparent within colloidal (>1 μm) fractions. Statisitcal (hierachical cluster) analysis of two particulate and three colloidal fractions from 23 samples from the MDRS is used as a basis to investigate geochemical and mineralogical associations within the particulate and colloidal size fractions and to provide additional supporting evidence for the conceptual isotopic/geochemical model.

Distributions of Virus-Like Particles and Prokaryotes within Microenvironments

Microbial interactions are important for ecosystem function, but occur at the microscale and so are difficult to observe. Previous studies in marine systems have shown significant shifts in microbial community abundance and composition over scales of micrometres to centimetres. This study investigates the microscale abundance distributions of virus-like particles (VLPs) and prokaryotes in the lower reaches of a river to determine the extent to which microscale microbial patchiness exists in freshwater systems. Here we report local hotspots surrounded by gradients that reach a maximum 80 and 107 fold change in abundance over 0.9 cm for prokaryotic and VLP subpopulations. Changes in prokaryotic and VLP hotspots were tightly coupled. There were no gradients at tens of centimetres across the boundary layers, which is consistent with strong mixing and turbulence-driven aggregation found in river systems. Quantification of the patchiness shows a marked asymmetry with patches 10 times greater than background common, but depletions being rare or absent in most samples. This consistent asymmetry suggests that coldspots depleted by grazing and lysis are rapidly mixed to background concentrations, while the prevalence of hotspots indicates persistence against disruption. The hotspot to coldspot relative abundance may be useful for understanding microbial river dynamics. The patchiness indicates that the mean- field approach of bulk phase sampling misses the microbially relevant community variation and may underestimate the concentrations of these important microbial groups.

Fibre evanescent field absorption (FEFA): an optical fibre technique for measuring light absorption in turbid water samples

An optical fibre technique for measuring the absorption of water-borne pigment in the present of significant suspended sediment concentration has been evaluated. Based on the absorption of the evanescent field of light propagating down a single glass (silica) fibre, the fibre evanescent field absorption (FEFA) technique has been demonstrated to be approximately 10-fold less sensitive to absorbing species than traditional bulk absorption methods. However, unlike traditional optical absorption measurements, the FEFA technique is insensitive to scattering by the suspended particles for particle concentrations expected in typical inland waters. A simple calculation estimates that this insensitivity persists for sediment concentrations up to 2000-fold those expected in Australian inland rivers. In addition to experimental results, a discussion of the potential operational use of this technique in measuring optical absorption properties of water containing suspended sediment is presented.

Persistence, loss and appearance of bacteria upstream and downstream of a river system

Bacterial taxa shape microbial community composition and influence aquatic ecosystem dynamics. Studies on bacterial persistence in rivers have primarily focussed on microbial-source tracking as an indicator for faecal-source contamination, whereas archetypal freshwater species have received minimal attention. The present study describes the river microbial communities upstream and 3.3km downstream of a small rural town. By 16S rDNA sequencing, we report three patterns in microbial community composition, namely, persistence, loss and appearance. Persistence was observed as 46% inter-site similarity, perhaps owing to generalists that have information lengths that exceed 3.3km and are capable of adapting to system fluctuations. Loss was observed as 10% site exclusivity upstream, perhaps owing to removal processes such as predation and lysis during transport downstream. Last, appearance was observed as 44% site exclusivity downstream, indicating potential anthropogenic impacts from land run-off on bacterial community composition. High multivariate dispersion among downstream samples, as well as overall sample dissimilarity, present as microscale hotspots of discrete Firmicutes and Cyanobacteria species, indicated higher heterogeneity downstream, and therefore increased patchiness from downstream transport and inputs of bacterial genotypes. These findings suggest relativities among three fates for bacterial species of fluvial systems, persistence, loss and appearance, with each having different effects on system dynamics.

Marine and giant viruses as indicators of a marine microbial community in a riverine system.

Viral communities are important for ecosystem function as they are involved in critical biogeochemical cycles and controlling host abundance. This study investigates riverine viral communities around a small rural town that influences local water inputs. Myoviridae, Siphoviridae, Phycodnaviridae, Mimiviridae, Herpesviridae, and Podoviridae were the most abundant families. Viral species upstream and downstream of the town were similar, with Synechoccocus phage, salinus, Prochlorococcus phage, Mimivirus A, and Human herpes 6A virus most abundant, contributing to 4.9–38.2% of average abundance within the metagenomic profiles, with Synechococcus and Prochlorococcus present in metagenomes as the expected hosts for the phage. Overall, the majority of abundant viral species were or were most similar to those of marine origin. At over 60 km to the river mouth, the presence of marine communities provides some support for the Baas‐Becking hypothesis “everything is everywhere, but, the environment selects.” We conclude marine microbial species may occur more frequently in freshwater systems than previously assumed, and hence may play important roles in some freshwater ecosystems within tens to a hundred kilometers from the sea.

Microbial micropatches within microbial hotspots

The spatial distributions of organism abundance and diversity are often heterogeneous. This includes the sub-centimetre distributions of microbes, which have ‘hotspots’ of high abundance, and ‘coldspots’ of low abundance. Previously we showed that 300 μl abundance hotspots, coldspots and background regions were distinct at all taxonomic levels. Here we build on these results by showing taxonomic micropatches within these 300 μl microscale hotspots, coldspots and background regions at the 1 μl scale. This heterogeneity among 1 μl subsamples was driven by heightened abundance of specific genera. The micropatches were most pronounced within hotspots. Micropatches were dominated by Pseudomonas, Bacteroides, Parasporobacterium and Lachnospiraceae incertae sedis, with Pseudomonas and Bacteroides being responsible for a shift in the most dominant genera in individual hotspot subsamples, representing up to 80.6% and 47.3% average abundance, respectively. The presence of these micropatches implies the ability these groups have to create, establish themselves in, or exploit heterogeneous microenvironments. These genera are often particle-associated, from which we infer that these micropatches are evidence for sub-millimetre aggregates and the aquatic polymer matrix. These findings support the emerging paradigm that the microscale distributions of planktonic microbes are numerically and taxonomically heterogeneous at scales of millimetres and less. We show that microscale microbial hotspots have internal structure within which specific local nutrient exchanges and cellular interactions might occur.

Inland water quality monitoring in Australia

Consistent and accurate information on inland water quality over wider areas of the Australian continent are required to assess current condition and trends in response to key environmental and climatic impacts. Optical remote sensing offers a method to objectively assess this over multiple spatial scales provided retrieval algorithms are accurate. Here, we present the results of initial research aimed at exploring the optical variability in Australian inland waters and of linear matrix inversion algorithms applied to both in situ reflectance spectra and high resolution satellite data to retrieve water inland water quality parameters. In situ sampling reveals a high degree of optical variability both within and between lakes across the regions sampled with regional patterns evident; sub-tropical and tropical lakes exhibited greater optical complexity than deep lakes in mid-latitude regions. Clustering analysis indicated the presence of 8 different optical water types in the water bodies measured. The ability of the linear matrix inversion algorithm to map water quality, tested on in situ reflectance and WorldView2 image datasets, showed relative accuracy when parameter sets were sufficient to achieve algorithm closure. Improved algorithm parameterization will be required to account for the high degree in spatial and temporal optical variability observed in Australian inland waters.