Forest top canopy bacterial communities are influenced by elevation and host tree traits.

BACKGROUND: The phyllosphere microbiome is crucial for plant health and ecosystem functioning. While host species play a determining role in shaping the phyllosphere microbiome, host trees of the same species that are subjected to different environmental conditions can still exhibit large degrees of variation in their microbiome diversity and composition. Whether these intra-specific variations in phyllosphere microbiome diversity and composition can be observed over the broader expanse of forest landscapes remains unclear. In this study, we aim to assess the variation in the top canopy phyllosphere bacterial communities between and within host tree species in the temperate European forests, focusing on Fagus sylvatica (European beech) and Picea abies (Norway spruce). RESULTS: We profiled the bacterial diversity, composition, driving factors, and discriminant taxa in the top canopy phyllosphere of 211 trees in two temperate forests, Veluwe National Parks, the Netherlands and Bavarian Forest National Park, Germany. We found the bacterial communities were primarily shaped by host species, and large variation existed within beech and spruce. While we showed that there was a core microbiome in all tree species examined, community composition varied with elevation, tree diameter at breast height, and leaf-specific traits (e.g., chlorophyll and P content). These driving factors of bacterial community composition also correlated with the relative abundance of specific bacterial families. CONCLUSIONS: While our results underscored the importance of host species, we demonstrated a substantial range of variation in phyllosphere bacterial diversity and composition within a host species. Drivers of these variations have implications at both the individual host tree level, where the bacterial communities differed based on tree traits, and at the broader forest landscape level, where drivers like certain highly plastic leaf traits can potentially link forest canopy bacterial community variations to forest ecosystem processes. We eventually showed close associations between forest canopy phyllosphere bacterial communities and host trees exist, and the consistent patterns emerging from these associations are critical for host plant functioning.

Environmental DNA highlights the influence of salinity and agricultural run-off on coastal fish assemblages in the Great Barrier Reef region.

Agricultural run-off in Australia's Mackay-Whitsunday region is a major source of nutrient and pesticide pollution to coastal and inshore ecosystems of the Great Barrier Reef. While the effects of run-off are well documented for the region's coral and seagrass habitats, the ecological impacts on estuaries, the direct recipients of run-off, are less known. This is particularly true for fish communities, which are shaped by the physico-chemical properties of coastal waterways that vary greatly in tropical regions. To address this knowledge gap, we used environmental DNA (eDNA) metabarcoding to examine fish assemblages at four locations (three estuaries and a harbour) subjected to varying levels of agricultural run-off during a wet and dry season. Pesticide and nutrient concentrations were markedly elevated during the sampled wet season with the influx of freshwater and agricultural run-off. Fish taxa richness significantly decreased in all three estuaries (F = 164.73, P = <0.001), along with pronounced changes in community composition (F = 46.68, P = 0.001) associated with environmental variables (largely salinity: 27.48% contribution to total variance). In contrast, the nearby Mackay Harbour exhibited a far more stable community structure, with no marked changes in fish assemblages observed between the sampled seasons. Among the four sampled locations, variation in fish community composition was more pronounced within the wet season (F = 2.5, P = 0.001). Notably, variation in the wet season was significantly correlated with agricultural contaminants (phosphorus: 6.25%, pesticides: 5.22%) alongside environmental variables (salinity: 5.61%, DOC: 5.57%). Historically contaminated and relatively unimpacted estuaries each demonstrated distinct fish communities, reflecting their associated catchment use. Our findings emphasise that while seasonal effects play a key role in shaping the community structure of fish in this region, agricultural contaminants are also important contributors in estuarine systems.

Monitoring the Health of Coastal Environments in the Pacific Region-A Review.

Coastal areas provide important ecological services to populations accessing, for example, tourism services, fisheries, minerals and petroleum. Coastal zones worldwide are exposed to multiple stressors that threaten the sustainability of receiving environments. Assessing the health of these valuable ecosystems remains a top priority for environmental managers to ensure the key stressor sources are identified and their impacts minimized. The objective of this review was to provide an overview of current coastal environmental monitoring frameworks in the Asia-Pacific region. This large geographical area includes many countries with a range of climate types, population densities and land uses. Traditionally, environmental monitoring frameworks have been based on chemical criteria set against guideline threshold levels. However, regulatory organizations are increasingly promoting the incorporation of biological effects-based data in their decision-making processes. Using a range of examples drawn from across the region, we provide a synthesis of the major approaches currently being applied to examine coastal health in China, Japan, Australia and New Zealand. In addition, we discuss some of the challenges and investigate potential solutions for improving traditional lines of evidence, including the coordination of regional monitoring programs, the implementation of ecosystem-based management and the inclusion of indigenous knowledge and participatory processes in decision-making.

Characterizing the spatial distributions of soil biota at a legacy base metal mine using environmental DNA.

Characterizing the distribution of biota in response to contaminants is a critical element of site risk assessments. In this study we investigated the spatial distributions of biota and soil chemistry data in surface soil from Sunny Corner, a legacy base metal sulfide mine, Australia. Our results showed that copper (Cu), zinc (Zn), arsenic (As) and lead (Pb) in the surface soil exceeded Australian national soil quality guidelines and posed risks to the environment. Environmental (e)DNA metabarcoding of prokaryote and eukaryote composition confirmed the suggestion of environmental risk posed by these elements collectively explaining 72.9 % and 60.5 % of the total variation in the composition of soil prokaryotes and eukaryotes, respectively. Prokaryotic taxa from the phyla Gemmatimonadetes, Verrucomicrobia and Deinococcus-Thermus showed similar spatial patterns to As and Pb, and were positively correlated. Eukaryotic taxa from the phylum Chlorophyta had similar positive correlations with As and Pb in the soil. In contrast, Amoebozoa and Cercozoa, were sensitive to metals and metalloids, having higher relative abundances in soils with lower concentrations of contaminants. Our study shows that metabarcoding is a promising ecological approach for rapid, large scale assessment of contaminated and potentially impacted sites.

Impact assessment of ephemeral discharge of contamination downstream of two legacy base metal mines using environmental DNA.

Mining and processing metalliferous ores can degrade the environment well beyond the footprint of the mine, particularly where on-site containment and post-mining remediation has been insufficient to prevent releases of solid and aqueous mine wastes. In this study, we investigated the potential of sediment and water chemistry coupled with environmental (e)DNA metabarcoding to evaluate discrete and cumulative ecological impacts of two legacy base metal (copper (Cu), zinc (Zn), lead (Pb)) mines (Peelwood and Cordillera) which discharge metals via ephemeral tributaries into perennial Peelwood Creek. Although the two mine streams exceeded Australian guidelines for sediment and freshwater quality for Cu, Zn and Pb, Peelwood Creek had relatively low sediment and water metal concentrations, suggesting a low potential for environmental toxicity. Although sediment and water chemistry defined the extent of biological impacts, metabarcoding showed that Peelwood and Cordillera mines had discrete impacts and Peelwood mine was the main source of contamination of Peelwood Creek. Metabarcoding showed that prokaryotes can be good indicators of metal contamination whereas eukaryotes did not reflect contamination impacts in Peelwood Creek. Metabarcoding results showed that benthic communities downstream of Cordillera mine were less impacted than those below Peelwood mine, suggesting that Peelwood mine should be considered for further remediation.

The use of diversity indices for local assessment of marine sediment quality.

Diversity indices are commonly used to measure changes in marine benthic communities. However, the reliability (and therefore suitability) of these indices for detecting environmental change is often unclear because of small sample size and the inappropriate choice of communities for analysis. This study explored uncertainties in taxonomic density and two indices of community structure in our target region, Japan, and in two local areas within this region, and explored potential solutions. Our analysis of the Japanese regional dataset showed a decrease in family density and a dominance of a few species as sediment conditions become degraded. Local case studies showed that species density is affected by sediment degradation at sites where multiple communities coexist. However, two indices of community structure could become insensitive because of masking by community variability, and small sample size sometimes caused misleading or inaccurate estimates of these indices. We conclude that species density is a sensitive indicator of change in marine benthic communities, and emphasise that indices of community structure should only be used when the community structure of the target community is distinguishable from other coexisting communities and there is sufficient sample size.

Application of environmental DNA for assessment of contamination downstream of a legacy base metal mine.

Acid Rock Drainage (ARD) from legacy mines can negatively impact the biota in sediments and waters for tens of kilometers downstream. Here we used environmental (e)DNA metabarcoding to assess the impacts of metal contaminants on biota in sediment and water downstream of a legacy base metal sulfide mine in southeastern Australia, as exemplar of similar mines elsewhere. Concentrations of metals in water were below Australian water quality guideline values at 20 km downstream for copper (Cu), 40 km downstream for zinc (Zn) and 10 km downstream for lead (Pb). Sediment metal concentrations were below national guideline concentrations at 10 km downstream for Cu, 60 km downstream for Zn and 20 km downstream for Pb. In contrast, metabarcoding showed that biological communities from sediment samples at 10 km and 20 km downstream were similar to sites close to the mine and thus indicative of being impacted, despite metal concentrations being relatively low. As we illustrate, when combined with sediment and water chemistry, metabarcoding can provide more ecological robust perspective on the downstream effects of legacy mines, capturing the sensitivities of a diverse range of organisms.

Metabarcoding Reveals Changes in Benthic Eukaryote and Prokaryote Community Composition along a Tropical Marine Sediment Nickel Gradient.

The Southeast Asia and Melanesia region has extensive nickel (Ni)-rich lateritic regoliths formed from the tropical weathering of ultramafic rocks. As the global demand for Ni continues to rise, these lateritic regoliths are increasingly being exploited for their economic benefit. Mining of these regoliths contributes to the enrichment of coastal sediments in trace metals, especially Ni. The present study used high-throughput sequencing (metabarcoding) to determine changes in eukaryote (18s v7 recombinant DNA [rDNA] and diatom-specific subregion of the 18s v4 rDNA) and prokaryote (16s v4 rDNA) community compositions along a sediment Ni concentration gradient offshore from a large lateritized ultramafic regolith in New Caledonia (Vavouto Bay). Significant changes in the eukaryote, diatom, and prokaryote community compositions were found along the Ni concentration gradient. These changes correlated most with the dilute-acid extractable concentration of Ni in the sediments, which explained 26, 23, and 19% of the variation for eukaryote, diatom, and prokaryote community compositions, respectively. Univariate analyses showed that there was no consistent change in indices of biodiversity, evenness, or richness. Diatom richness and diversity did, however, decrease as sediment acid extractable-Ni concentrations increased. Threshold indicator taxa analysis was conducted separately for each of the 3 targeted genes to detect changes in taxa whose occurrences decreased or increased along the acid extractable-Ni concentration gradient. Based on these data, 46 mg acid extractable-Ni/kg was determined as a threshold value where sensitive species began to disappear. In the case of the estuarine sediments offshore from lateritized ultramafic regolith in New Caledonia, this is recommended as an interim threshold value until further lines of evidence can contribute to a region-specific Ni sediment quality guideline value. Environ Toxicol Chem 2021;40:1894-1907. © 2021 SETAC.

Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems.

Loss of biodiversity from lower to upper trophic levels reduces overall productivity and stability of coastal ecosystems in our oceans, but rarely are these changes documented across both time and space. The characterisation of environmental DNA (eDNA) from sediment and seawater using metabarcoding offers a powerful molecular lens to observe marine biota and provides a series of 'snapshots' across a broad spectrum of eukaryotic organisms. Using these next-generation tools and downstream analytical innovations including machine learning sequence assignment algorithms and co-occurrence network analyses, we examined how anthropogenic pressures may have impacted marine biodiversity on subtropical coral reefs in Okinawa, Japan. Based on 18 S ribosomal RNA, but not ITS2 sequence data due to inconsistent amplification for this marker, as well as proxies for anthropogenic disturbance, we show that eukaryotic richness at the family level significantly increases with medium and high levels of disturbance. This change in richness coincides with compositional changes, a decrease in connectedness among taxa, an increase in fragmentation of taxon co-occurrence networks, and a shift in indicator taxa. Taken together, these findings demonstrate the ability of eDNA to act as a barometer of disturbance and provide an exemplar of how biotic networks and coral reefs may be impacted by anthropogenic activities.

Social Barriers in Ecological Landscapes: The Social Resistance Hypothesis.

Across animal societies, individuals invest time and energy in social interactions. The social landscape that emerges from these interactions can then generate barriers that limit the ability of individuals to disperse to, and reproduce in, groups or populations. Therefore, social barriers can contribute to the difference between the physical capacity for movement through the habitat and subsequent gene flow. We call this contributing effect 'social resistance'. We propose that social resistance can act as an agent of selection on key life-history strategies and promote the evolution of social strategies that facilitate effective dispersal. By linking landscape genetics and social behaviour, the social resistance hypothesis generates predictions integrating dispersal, connectivity, and life-history evolution.

The effect of dissolved nickel and copper on the adult coral Acropora muricata and its microbiome.

The potential impacts of mining activities on tropical coastal ecosystems are poorly understood. In particular, limited information is available on the effects of metals on scleractinian corals which are foundation species that form vital structural habitats supporting other biota. This study investigated the effects of dissolved nickel and copper on the coral Acropora muricata and its associated microbiota. Corals collected from the Great Barrier Reef were exposed to dissolved nickel (45, 90, 470, 900 and 9050 µg Ni/L) or copper (4, 11, 32 and 65 µg Cu/L) in flow through chambers at the National Sea Simulator, Townsville, Qld, Australia. After a 96-h exposure DNA metabarcoding (16S rDNA and 18S rDNA) was undertaken on all samples to detect changes in the structure of the coral microbiome. The controls remained healthy throughout the study period. After 36 h, bleaching was only observed in corals exposed to 32 and 65 µg Cu/L and very high nickel concentrations (9050 µg Ni/L). At 96 h, significant discolouration of corals was only observed in 470 and 900 µg Ni/L treatments, the highest concentrations tested. While high concentrations of nickel caused bleaching, no changes in the composition of their microbiome communities were observed. In contrast, exposure to copper not only resulted in bleaching, but altered the composition of both the eukaryote and bacterial communities of the coral's microbiomes. Our findings showed that these effects were only evident at relatively high concentrations of nickel and copper, reflecting concentrations observed only in extremely polluted environments. Elevated metal concentrations have the capacity to alter the microbiomes which are inherently linked to coral health.

Using Bayesian networks to predict risk to estuary water quality and patterns of benthic environmental DNA in Queensland.

Predictive modeling can inform natural resource management by representing stressor-response pathways in a logical way and quantifying the effects on selected endpoints. This study demonstrates a risk assessment model using the Bayesian network relative risk model (BN-RRM) approach to predict water quality and, for the first time, eukaryote environmental DNA (eDNA) data as a measure of benthic community structure. Environmental DNA sampling is a technique for biodiversity measurements that involves extracting DNA from environmental samples, amplicon sequencing a targeted gene, in this case the 18s rDNA gene (which targets eukaryotes), and matching the sequences to organisms. Using a network of probability distributions, the BN-RRM model predicts risk to water quality objectives and the relative richness of benthic taxa groups in the Noosa, Pine, and Logan estuaries in Southeast Queensland (SEQ), Australia. The model predicts Dissloved Oxygen more accurately than the chlorophyll a water quality endpoint and photosynthesizing benthos more accurately than heterotrophs. Results of BN-RRM modeling given current inputs indicate that the water quality and benthic assemblages of the Noosa are relatively homogenous across all sub risk regions, and that the Noosa has a 73%-92% probability of achieving water quality objectives, indicating a low relative risk. Conversely, the Middle Logan, Middle Pine, and Lower Pine regions are much less likely to meet objectives (15%-55% probability), indicating a relatively higher risk to water quality in those regions. The benthic community richness patterns associated with risk in the Noosa are high Diatom relative richness and low Green Algae relative richness. The only benthic pattern consistently associated with the relatively higher risk to water quality is high richness of fungi species. The BN-RRM model provides a basis for future predictions and adaptive management at the direction of resource managers. Integr Environ Assess Manag 2019;15:93-111. © 2018 SETAC.

Trophic transfer of metals in a seagrass food web: Bioaccumulation of essential and non-essential metals.

Metal concentrations are reported for a seagrass ecosystem receiving industrial inputs. δ13C and δ15N isotope ratios were used to establish trophic links. Copper concentrations (dry mass) ranged from <0.01 µg/g in fish species to 570 µg/g (µâ€¯= 49 ±â€¯SD = 90 µg/g) in the oyster Saccostrea glomerata. Zinc concentrations ranged from 0.6 µg/g in the seagrass Zostera capricorni to 10,800 µg/g in the mud oyster Ostrea angasi (µâ€¯= 434 ±â€¯1390 µg/g). Cadmium concentrations ranged from <0.01 µg/g in fish species to 268 µg/g in Ostrea angasi (µâ€¯= 6 ±â€¯25 µg/g). Lead concentrations ranged from <0.01 µg/g for most fish species to 20 µg/g in polychaetes (µâ€¯= 2 ±â€¯3 µg/g). Biomagnification of metals did not occur. Organisms that fed on particulate organic matter and benthic microalgae had higher metal concentrations than those that fed on detritus. Species physiology also played an important role in the bioaccumulation of metals.

Effects of micronized and nano-copper azole on marine benthic communities.

The widespread use of copper nanomaterials (CuNMs) as antibacterial and antifouling agents in consumer products increases the risk for metal contamination and adverse effects in aquatic environments. Information gaps exist on the potential toxicity of CuNMs in marine environments. We exposed field-collected marine meio- and macrobenthic communities to sediments spiked with micronized copper azole (MCA) using a novel method that brings intact benthic cores into the laboratory and exposes the organisms via surface application of sediments. Treatments included field and laboratory controls, 3 spiked sediments: low-MCA (51.9 mg/kg sediment), high-MCA (519 mg/kg sediment), and CuSO4 (519 mg/kg sediment). In addition, single-species acute testing was performed with both MCA and CuSO4. Our results indicate that meio- and macrofaunal assemblages exposed to High-MCA and CuSO4 treatments differed significantly from both the laboratory control and the low-MCA treatments. Differences in macrofauna were driven by decreases in 3 Podocopa ostracod species, the bivalve Gemma gemma, and the polychaetes Exogone verugera and Prionospio heterobranchia relative to the laboratory control. Differences in the meiofaunal community are largely driven by nematodes. The benthic community test results were more sensitive than the single-species test results. Findings of this investigation indicate that CuNMs represent a source of risk to marine benthic communities comparable to that of dissolved Cu. Environ Toxicol Chem 2018;37:362-375. Published 2017 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.

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.

Effects of uranium concentration on microbial community structure and functional potential.

Located in the Northern Territory of Australia, Ranger uranium mine is directly adjacent to the UNESCO World Heritage listed Kakadu National Park, with rehabilitation targets needed to ensure the site can be incorporated into the park following the mine's closure in 2026. This study aimed to understand the impact of uranium concentration on microbial communities, in order to identify and describe potential breakpoints in microbial ecosystem services. This is the first study to report in situ deployment of uranium-spiked sediments along a concentration gradient (0-4000 mg U kg-1 ), with the study design maximising the advantages of both field surveys and laboratory manipulative studies. Changes to microbial communities were characterised through the use of amplicon and shotgun metagenomic next-generation sequencing. Significant changes to taxonomic and functional community assembly occurred at a concentration of 1500 mg U kg-1 sediment and above. At uranium concentrations of ≥ 1500 mg U kg-1 , genes associated with methanogenic consortia and processes increased in relative abundance, while numerous significant changes were also seen in the relative abundances of genes involved in nitrogen cycling. Such alterations in carbon and nitrogen cycling pathways suggest that taxonomic and functional changes to microbial communities may result in changes in ecosystem processes and resilience.

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.

Time-averaged copper concentrations from continuous exposures predicts pulsed exposure toxicity to the marine diatom, Phaeodactylum tricornutum: Importance of uptake and elimination.

Intermittent, fluctuating and pulsed contaminant discharges result in organisms receiving highly variable contaminant exposures. Current water quality guidelines are predominantly derived using data from continuous exposure toxicity tests, and most frequently applied by regulators with the assumption that concentrations from a single sampling event will provide a meaningful approach to assessing potential effects. This study investigated the effect of single and multiple (daily) dissolved copper pulses on the marine diatom, Phaeodactylum tricornutum, including measurements of copper uptake and elimination to investigate the toxic mechanism. Copper pulses of between 0.5 and 24h and continuous exposures with equivalent 72-h time-averaged concentrations (TACs) resulted in similar biomass inhibition of P. tricornutum, with continuous exposures often being marginally more toxic. Rates of cell division generally recovered to control levels within 24h of the copper pulse removal. Upon resuspension in clean seawater, the extracellular copper per cell decreased rapidly, whereas the intracellular copper per cell decreased slowly. Negligible loss of copper from the total algal biomass indicated that P. tricornutum did not have an effective mechanism for eliminating copper from cells, rather the intracellular copper decreased as a result of dilution by cellular division as the algal growth rate recovered. The measurement of copper uptake after 72-h exposure and kinetics of elimination thereafter suggest that continuous exposures are marginally more toxic to P. tricornutum than pulsed copper exposures with equivalent TACs because slow internalization and saturation of algal membrane transport sites results in less copper uptake into pulse-exposed cells than continuously-exposed cells coupled with dilution of internalized copper via cellular division in the post-exposure period. In the case of P. tricornutum, the results indicate that water quality guidelines for copper based on continuous exposure will be conservative when applied to short-term discharges.

Direct and indirect effects of copper-contaminated sediments on the functions of model freshwater ecosystems.

Copper is acutely toxic to, and directly affects, primary producers and decomposers, which are key players in essential processes such as the nutrient cycle in freshwater ecosystems. Even though the indirect effects of metals (for example effects due to changes in species interactions) may be more common than direct effects, little is known about the indirect effects of copper on primary producers and decomposers. The effects of copper on phytoplankton, macrophytes, periphyton and organic matter decomposition in an outdoor lentic mesocosm facility were assessed, and links between the responses examined. Copper directly decreased macrophyte growth, subsurface organic matter decomposition, and the potential for high phytoplankton Chlorophyll a concentrations. However, periphyton cover and organic matter decomposition on the surface of the sediment were stimulated by the presence of copper. These latter responses were attributed to indirect effects, due to a reduction in grazing pressure from snails, particularly Physa acuta, in the higher copper-contaminated mesocosms. This permitted the growth of periphyton and other heterotrophs, ultimately increasing decomposition at the sediment surface. The present study demonstrates the pronounced influence indirect effects may have on ecological function, findings that may not be observed in traditional laboratory studies (which utilize single species or simplistic communities).