Field survey,isolation, identification and pathogenicity of Phytophthora species associated with a Mediterranean‐type tree species

Corymbia calophylla (marri), a keystone tree species in the global biodiversity hot spot of southwestern Australia, is suffering decline and mortality associated with a canker disease caused by the endemic fungus Quambalaria coyrecup. Phytophthora species are frequently isolated from the rhizosphere of C. calophylla, and a hypothesis is that Phytophthora root infection is predisposing C. calophylla to this endemic canker pathogen. Field surveys were conducted in both anthropogenically disturbed and undisturbed C. calophylla stands, from where a total of 100 rhizosphere soil samples, from both healthy and cankered trees, were collected. Phytophthora species were isolated from 26% of the samples collected, with Phytophthora incidence significantly higher on disturbed stands than in natural forests (73% and 27%, respectively). Five Phytophthora species were recovered, including P. cinnamomi, P. elongata, P. multivora, P. pseudocryptogea and P. versiformis. Under‐bark inoculations with the Phytophthora isolates caused significant lesion lengths in excised C. calophylla stems. Corymbia calophylla response to pot infestation trials in the glasshouse varied between Phytophthora species and isolates, with isolates of P. cinnamomi and P. multivora causing a significant reduction in seedling root volume and often leading to seedling death. This study demonstrates that root disease caused by Phytophthora species, especially P. cinnamomi and P. multivora, has the ability to adversely affect C. calophylla health. This study leads the way to do a dual inoculation trial with the canker pathogen Q. coyrecup, and different Phytophthora species to investigate if Phytophthora root infection predisposes C. calophylla to this canker disease.     

Habitat associations of the Threatened pugnose minnow (Opsopoeodus emiliae) at the northern edge of the species range

Pugnose minnow (Opsopoeodus emiliae) is a small, reclusive species that is widespread in North America, but is one of the rarest fishes in Canada, found in less than 12 known localities in southwestern Ontario. In contrast to most pugnose minnow populations across the global range, Canadian populations are primarily found in turbid systems, potentially indicating persistence in suboptimal conditions. We used data from a multi-gear species and habitat survey in the Canard River, Ontario, a system dominated by agricultural inputs and the best-known capture site of the species in Canada, to parameterise multi-gear occupancy models for understanding the relationship between pugnose minnow occupancy and microhabitat features, including the role of turbidity. Almost 300 pugnose minnow were captured, representing the largest single collection of the species in Canadian history. The best occupancy model indicated that the probability of pugnose minnow occupancy was highest in the deepest sites with the lowest water clarity (i.e. high turbidity); however, competing models suggested that occupancy was highest at sites with wild celery (Vallisneria americana) and higher water clarity, signifying that habitats with low turbidity may be utilised if sufficient physical cover exists. Together, our results suggest that Canadian pugnose minnow populations occupy and potentially favour turbid conditions, possibly to avoid visual predators in clearer habitats. It remains uncertain whether this abiotic association represents a long-term, viable, local adaptation or whether persistence of pugnose minnow in the Canard River is at risk unless significant water quality improvements can be made.     

Using systematic conservation planning to establish management priorities for freshwater salmon conservation,Matanuska‐Susitna Basin,AK, USA

1. The Alaskan Matanuska‐Susitna Basin (MSB) provides habitat for all five Pacific salmon species, and their large seasonal spawning runs are important both ecologically and economically. However, the encroachment of human development through urbanization and extractive industries poses a serious risk to salmon habitat in the MSB.
2. Using systematic conservation planning techniques, different methods of incorporating anthropogenic risks were assessed to determine how to conserve salmon habitat in the area cost‐effectively.
3. The consequences of four distinct conservation scenarios were quantified: no consideration either of urbanization or extractive industries (‘Risk ignored’ scenario); accounting for the risk of urbanization, and avoiding conservation in all areas rich in fossil fuels (‘Urbanization accounted, all extraction avoided’ scenario); accounting for urbanization and oil and gas development, but avoiding conservation in coal‐rich areas (‘Urbanization accounted, coal areas avoided’ scenario); and accounting for all anthropogenic risks to habitat, and allowing conservation in oil, gas, or coal‐rich areas (‘All risks accounted’ scenario). To compare conservation success and resilience, the impacts of these risks were estimated using Monte Carlo simulations. The final cost of each solution was then divided by the number of conservation targets met to determine a return on investment.
4. Results from scenarios that avoided all extractive activities, or only coal, suggest that conservation targets cannot be met simply by avoiding areas rich in fossil fuels, and these scenarios resulted in lower returns on investment than those in which risks from extraction were incorporated into the solution.
5. By developing a method for setting priorities that are economically based, this study provides a method for local managers and conservation groups to identify conservation opportunities in MSB river basins.

     

Historical patterns of fire severity and forest structure and composition in a landscape structured by frequent large fires: Pumice Plateau ecoregion,Oregon, USA

Context

Lack of quantitative observations of extent, frequency, and severity of large historical fires constrains awareness of departure of contemporary conditions from those that demonstrated resistance and resilience to frequent fire and recurring drought.

Objectives

Compare historical and contemporary fire and forest conditions for a dry forest landscape with few barriers to fire spread.

Methods

Quantify differences in (1) historical (1700–1918) and contemporary (1985–2015) fire extent, fire rotation, and stand-replacing fire and (2) historical (1914–1924) and contemporary (2012) forest structure and composition. Data include 85,750-ha tree-ring reconstruction of fire frequency and extent; >?375,000-ha timber inventory following >?78,900-ha fires in 1918; and remotely-sensed maps of contemporary fire effects and forest conditions.

Results

Historically, fires?>?20,000 ha occurred every 9.5 years; fire rotation was 14.9 years; seven fires?>?40,469 ha occurred during extreme drought (PDSI <?? 4.0); and stand-replacing fire occurred primarily in lodgepole (Pinus contorta var. murrayana). In contemporary fires, only 5% of the ecoregion burned in 30 years, and stand-replacing fire occurred primarily in ponderosa (Pinus ponderosa) and mixed-conifer. Historically, density of conifers?>?15 cm dbh exceeded 120 trees/ha on?<?5% of the area compared to 95% currently.

Conclusions

Frequent, large, low-severity fires historically maintained open-canopy ponderosa and mixed-conifer forests in which large fire- and drought-tolerant trees were prevalent. Stand-replacing patches in ponderosa and mixed-conifer were rare, even in fires >?40,469 ha (minimum size of contemporary “megafires”) during extreme drought. In this frequent-fire landscape, mixed-severity fire historically influenced lodgepole and adjacent forests. Lack of large, frequent, low-severity fires degrades contemporary forest ecosystems.

     

Simulation modelling of potato virus Y spread in relation to initial inoculum and vector activity

Potato virus Y(PVY) is a non-persistent virus that is transmitted by many aphid species and causes significant damage to potato production. We constructed a spatially-explicit model simulating PVY spread in a potato field and used it to investigate possible effects of transmission efficiency, initial inoculum levels, vector behavior, vector abundance, and timing of peak vector activity on PVY incidence at the end of a simulated growing season. Lower PVY incidence in planted seed resulted in lower virus infection at the end of the season. However, when populations of efficient PVY vectors were high, significant PVY spread occurred even when initial virus inoculum was low. Non-colonizing aphids were more important for PVY spread compared to colonizing aphids, particularly at high densities. An early-season peak in the numbers of noncolonizing aphids resulted in the highest number of infected plants in the end of the season, while mid-and late-season peaks caused relatively little virus spread. Our results highlight the importance of integrating different techniques to prevent the number of PVY-infected plants from exceeding economically acceptable levels instead of trying to control aphids within potato fields. Such management plans should be implemented very early in a growing season.     

Macroalgal meadow habitats support fish and fisheries in diverse tropical seascapes

Canopy‐forming macroalgae can construct extensive meadow habitats in tropical seascapes occupied by fishes that span a diversity of taxa, life‐history stages and ecological roles. Our synthesis assessed whether these tropical macroalgal habitats have unique fish assemblages, provide fish nurseries and support local fisheries. We also applied a meta‐analysis of independent surveys across 23 tropical reef locations in 11 countries to examine how macroalgal canopy condition is related to the abundance of macroalgal‐associated fishes. Over 627 fish species were documented in tropical macroalgal meadows, with 218 of these taxa exhibiting higher local abundance within this habitat (cf. nearby coral reef) during at least one life‐history stage. Major overlap (40%–43%) in local fish species richness among macroalgal and seagrass or coral reef habitats suggest macroalgal meadows may provide an important habitat refuge. Moreover, the prominence of juvenile fishes suggests macroalgal meadows facilitate the triphasic life cycle of many fishes occupying diverse tropical seascapes. Correlations between macroalgal canopy structure and juvenile abundance suggests macroalgal habitat condition can influence levels of replenishment in tropical fish populations, including the majority of macroalgal‐associated fishes that are targeted by commercial, subsistence or recreational fisheries. While many macroalgal‐associated fishery species are of minor commercial value, their local importance for food and livelihood security can be substantial (e.g. up to 60% of landings in Kenyan reef fisheries). Given that macroalgal canopy condition can vary substantially with sea temperature, there is a high likelihood that climate change will impact macroalgal‐associated fish and fisheries.     

A highly sensitive,non‐invasive qPCR‐based strategy for direct quantification of Yersinia ruckeri in fish faeces

Finfish with asymptomatic Yersinia ruckeri infections pose a major risk as they can transmit the pathogen and cause clinical outbreaks in stock populations. Current tools have insufficient quantitative ability for accurately detecting the trace levels of Y. ruckeri typically associated with asymptomatic infection, necessitate invasive or lethal sampling, or require long processing times. This study presents a highly sensitive qPCR‐based method, targeting part of the Y. ruckeri 16S rRNA sequence, that is capable of detecting extremely low levels of Y. ruckeri in noninvasively collected faecal samples. Quantitative precision and accuracy of faecal sample analysis was consistent, despite the complexity of the faecal matrix. The assay demonstrated linearity over a six log‐wide dynamic range. Its limit of detection (LOD) and limit of quantification (LOQ) were 4 and 10 copies of the target sequence, respectively. Sensitivity of the assay was comparable to other qPCR‐based methods without requiring invasive or lethal sampling. Applicability as a screening strategy was tested using passively collected faecal samples. Asymptomatic Y. ruckeri infection was detected in all samples, although none of the fish exhibited overt infection. This method will be beneficial for finfish disease management if developed further as a noninvasive, screening tool against asymptomatic Y. ruckeri infection.     

Nutrient limitations to bacterial and fungal growth during cellulose decomposition in tropical forest soils

Nutrients constrain the soil carbon cycle in tropical forests, but we lack knowledge on how these constraints vary within the soil microbial community. Here, we used in situ fertilization in a montane tropical forest and in two lowland tropical forests on contrasting soil types to test the principal hypothesis that there are different nutrient constraints to different groups of microorganisms during the decomposition of cellulose. We also tested the hypotheses that decomposers shift from nitrogen to phosphorus constraints from montane to lowland forests, respectively, and are further constrained by potassium and sodium deficiency in the western Amazon. Cellulose and nutrients (nitrogen, phosphorus, potassium, sodium, and combined) were added to soils in situ, and microbial growth on cellulose (phospholipid fatty acids and ergosterol) and respiration were measured. Microbial growth on cellulose after single nutrient additions was highest following nitrogen addition for fungi, suggesting nitrogen as the primary limiting nutrient for cellulose decomposition. This was observed at all sites, with no clear shift in nutrient constraints to decomposition between lowland and montane sites. We also observed positive respiration and fungal growth responses to sodium and potassium addition at one of the lowland sites. However, when phosphorus was added, and especially when added in combination with other nutrients, bacterial growth was highest, suggesting that bacteria out-compete fungi for nitrogen where phosphorus is abundant. In summary, nitrogen constrains fungal growth and cellulose decomposition in both lowland and montane tropical forest soils, but additional nutrients may also be of critical importance in determining the balance between fungal and bacterial decomposition of cellulose.