Review of coast and marine ecosystems in temperate Australia demonstrates a wealth of ecosystem services

© Copyright © 2020 Gaylard, Waycott and Lavery. Temperate Australia has extensive and diverse coast and marine habitats throughout its inshore and offshore waters. The region includes the southernmost extent of mangroves, over 500 estuaries and coastal embayments, home to extensive meadows of seagrasses and tidal saltmarsh. In areas of hard substrate, rocky reefs are abundant and productive with large forests of macroalgae. Coastal regions can be densely populated by humans and often habitats can be degraded, polluted or lost, while some remain relatively isolated and pristine. These habitats provide services to society including provision of food, regulate our climate through sequestration of carbon, treating our waste and protecting our shorelines from damage from storms. Coastal areas are culturally importantly hubs for recreation and tourism. Habitat mapping demonstrates diverse habitats throughout temperate Australia, but a formal investigation of services provided by these habitats has been lacking. This review of ecosystem services provided by coast and marine environments throughout temperate Australia reveals vast and productive ecosystems that provide multiple ecosystem services, substantial value to the Australian economy and contribute to the health and well-being of people who live in, visit of benefit from services or products from these regions. Some of these are considered within traditional economic metrics such as provision of wild catch fisheries, but this review demonstrates that regulation and maintenance services including waste treatment and protecting shorelines from extreme events are under recognized, and their value is substantial. However, consistent with many locations globally, coast and marine habitats are under threat from increasing development, sewage, agricultural, industrial discharges, urban runoff and climate change. Resultantly, temperate Australian coast and marine habitat extent and condition is generally declining in many regions, putting the provision of services and benefits to the community at risk. Continued degraded or lost habitats indicate current management frameworks are not capturing the full risk from development and there are winners and losers in trade off decision making. Incorporating ecosystem services in decision making may allow an integrated approach to management, and acknowledgment of services provided could prevent habitats from being undervalued against economic and social interests, a practice that often results in environmental degradation

A framework for the resilience of seagrass ecosystems

Seagrass ecosystems represent a global marine resource that is declining across its range. To halt degradation and promote recovery over large scales, management requires a radical change in emphasis and application that seeks to enhance seagrass ecosystem resilience. In this review we examine how the resilience of seagrass ecosystems is becoming compromised by a range of local to global stressors, resulting in ecological regime shifts that undermine the long-term viability of these productive ecosystems. To examine regime shifts and the management actions that can influence this phenomenon we present a conceptual model of resilience in seagrass ecosystems. The model is founded on a series of features and modifiers that act as interacting influences upon seagrass ecosystem resilience. Improved understanding and appreciation of the factors and modifiers that govern resilience in seagrass ecosystems can be utilised to support much needed evidence based management of a vital natural resource

Genetic variability within seagrass of the north west of Western Australia: Report of Theme 5 - Project 5.2 prepared for the Dredging Science Node

The response of seagrass species to on-going pressures such as dredging can be strongly influenced by their ability to adapt to, resist or recover from these pressures. The ability of species to adapt to a pressure, over generations, is influenced by the amount of genetic variation in a population: greater genetic diversity can enhance resistance and higher levels of gene flow between populations can enhance the rate of recovery following complete habitat loss. As seagrass are clonal plants, genetic diversity in a meadow is dependent on both the number of unique clones within the meadow, and distribution of this variation within and among meadows. Understanding the genetic diversity of seagrass meadows can provide important fundamental knowledge for the prediction of dredging impacts, by providing insights into the likelihood of recovery and the processes that may drive that recovery (vegetative regrowth, seed bank recruitment or immigration of recruits). It can also inform management, for example by providing insights into relative vulnerability to pressures, sources of recruitment populations and the importance of maintaining seed banks. However, for most seagrasses and in most parts of the world, extremely little is known about the genetic diversity and connectivity of populations..

Vulnerability of coastal and estuarine habitats in the GBR to climate change

Coastal and estuarine habitats occupy a central place in the functioning of tropical marine ecosystems. Their location at the interface between land and sea means they function to modulate the movement of terrestrial materials (eg freshwater, nutrients and pollutants) into the marine environment. Coastal and estuarine habitats also act as a filter, with functional units such as mangrove forests inhibiting trapping and retaining sediments and nutrients. Coastal habitats are also crucial nursery grounds for many species of fish111 and crustaceans, and act as links in the life cycles of species that migrate between marine and freshwater habitats. Beyond this, their close proximity to population and industrial centres makes them the marine habitats most vulnerable to human impacts. The east coast of tropical Queensland comprises a diversity of habitats, ranging from freshwater and littoral marshes, through estuaries, to nearshore open oceans and reefs. These habitats do not function alone but are an interlinked coastal ecosystem mosaic (CEM), connected at a variety of spatial, temporal, functional and conceptual scales. This complex mix of habitats is inhabited by one of the most diverse faunas on earth with organisms covering the full taxonomic spectrum, from viruses and bacteria to cetaceans. Unfortunately, detailed ecological knowledge is limited to a very small subset of the range of these organisms, with many species unknown, unidentified or unquantified. Although it is clear species interact in complex ways, our understanding of this is critically deficient. Moreover, many of the individual components are poorly understood, and details of the links between them largely absent

The risk of multiple anthropogenic and climate change threats must be considered for continental scale conservation and management of seagrass habitat

Globally marine-terrestrial interfaces are highly impacted due to a range of human pressures. Seagrass habitats exist in the shallow marine waters of this interface, have significant values and are impacted by a range of pressures. Cumulative risk analysis is widely used to identify risk from multiple threats and assist in prioritizing management actions. This study conducted a cumulative risk analysis of seagrass habitat associated with the Australian continent to support management actions. We developed a spatially explicit risk model based on a database of threats to coastal aquatic habitat in Australia, spanning 35,000 km of coastline. Risk hotspots were identified using the model and reducing the risk of nutrient and sediment pollution for seagrass habitat was assessed. Incorporating future threats greatly altered the spatial-distribution of risk. High risk from multiple current threats was identified throughout all bioregions, but high risk from climate change alone manifested in only two. Improving management of nutrient and sediment loads, a common approach to conserve seagrass habitat did reduce risk, but only in temperate regions, highlighting the danger of focusing management on a single strategy. Monitoring, management and conservation actions from a national and regional perspective can be guided by these outputs

Advancing DNA barcoding and metabarcoding applications for plants requires systematic analysis of herbarium collections-an Australian perspective

Building DNA barcode databases for plants has historically been ad hoc, and often with a relatively narrow taxonomic focus. To realize the full potential of DNA barcoding for plants, and particularly its application to metabarcoding for mixed-species environmental samples, systematic sequencing of reference collections is required using an augmented set of DNA barcode loci, applied according to agreed data generation and analysis standards. The largest and most complete reference collections of plants are held in herbaria. Australia has a globally significant flora that is well sampled and expertly curated by its herbaria, coordinated through the Council of Heads of Australasian Herbaria. There exists a tremendous opportunity to provide a comprehensive and taxonomically robust reference database for plant DNA barcoding applications by undertaking coordinated and systematic sequencing of the entire flora of Australia utilizing existing herbarium material. In this paper, we review the development of DNA barcoding and metabarcoding and consider the requirements for a robust and comprehensive system. We analyzed the current availability of DNA barcode reference data for Australian plants, recommend priority taxa for database inclusion, and highlight future applications of a comprehensive metabarcoding system. We urge that large-scale and coordinated analysis of herbarium collections be undertaken to realize the promise of DNA barcoding and metabarcoding, and propose that the generation and curation of reference data should become a national investment priority

A Multi-Gene Region Targeted Capture Approach to Detect Plant DNA in Environmental Samples: A Case Study From Coastal Environments

Published: 25 October 2021Metabarcoding of plant DNA recovered from environmental samples, termed environmental DNA (eDNA), has been used to detect invasive species, track biodiversity changes, and reconstruct past ecosystems. The P6 loop of the trnL intron is the most widely utilised gene region for metabarcoding plants due to the short fragment length and subsequent ease of recovery from degraded DNA, which is characteristic of environmental samples. However, the taxonomic resolution for this gene region is limited, often precluding species level identification. Additionally, targeting gene regions using universal primers can bias results as some taxa will amplify more effectively than others. To increase the ability of DNA metabarcoding to better resolve flowering plant species (angiosperms) within environmental samples, and reduce bias in amplification, we developed a multi-gene targeted capture method that simultaneously targets 20 chloroplast gene regions in a single assay across all flowering plant species. Using this approach, we effectively recovered multiple chloroplast gene regions for three species within artificial DNA mixtures down to 0.001 ng/mL of DNA. We tested the detection level of this approach, successfully recovering target genes for 10 flowering plant species. Finally, we applied this approach to sediment samples containing unknown compositions of eDNA and confidently detected plant species that were later verified with observation data. Targeting multiple chloroplast gene regions in environmental samples, enabled species-level information to be recovered from complex DNA mixtures. Thus, the method developed here, confers an improved level of data on community composition, which can be used to better understand flowering plant assemblages in environmental samples.Nicole R. Foster, Kor-jent van Dijk, Ed Biffin, Jennifer M. Young, Vicki A. Thomson, Bronwyn M. Gillanders, Alice R. Jones and Michelle Waycot

The secret hidden in dust:Assessing the potential to use biological and chemical properties of the airborne fraction of soil for provenance assignment and forensic casework

The airborne fraction of soil (dust) is both ubiquitous in nature and contains localised biological and chemical signatures, making it a potential medium for forensic intelligence. Metabarcoding of dust can yield biological communities unique to the site of interest, similarly, geochemical analyses can uncover elements and minerals within dust that can be matched to a geographic location. Combining these analyses presents multiple lines of evidence as to the origin of dust collected from items of interest. In this work, we investigated whether bacterial and fungal communities in dust change through time and whether they are comparable to soil samples of the same site. We integrated dust metabarcoding into a framework amenable to forensic casework, (i.e., using calibrated log-likelihood ratios) to predict the origin of dust samples using models constructed from both dust samples and soil samples from the same site. Furthermore, we tested whether both metabarcoding and geochemical/mineralogical analyses could be conducted on a single swabbed sample, for situations where sampling is limited. We found both analyses could generate results from a single swabbed sample and found biological and chemical signatures unique to sites. However, we did find significant variation within sites, where this did not always correlate with time but was a random effect of sampling. This variation within sites was not greater than between sites and so did not influence site discrimination. When modelling bacterial and fungal diversity using calibrated log-likelihood ratios, we found samples were correctly predicted using dust 67% and 56% of the time and using soil 56% and 22% of the time for bacteria and fungi communities respectively. Incorrect predictions were related to within site variability, highlighting limitations to assigning dust provenance using metabarcoding of soil.</p

The movement ecology of seagrasses

A movement ecology framework is applied to enhance our understanding of the causes, mechanisms and consequences of movement in seagrasses: marine, clonal, flowering plants. Four life-history stages of seagrasses can move: pollen, sexual propagules, vegetative fragments and the spread of individuals through clonal growth. Movement occurs on the water surface, in the water column, on or in the sediment, via animal vectors and through spreading clones. A capacity for long-distance dispersal and demographic connectivity over multiple timeframes is the novel feature of the movement ecology of seagrasses with significant evolutionary and ecological consequences. The space–time movement footprint of different life-history stages varies. For example, the distance moved by reproductive propagules and vegetative expansion via clonal growth is similar, but the timescales range exponentially, from hours to months or centuries to millennia, respectively. Consequently, environmental factors and key traits that interact to influence movement also operate on vastly different spatial and temporal scales. Six key future research areas have been identified