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Highlights • Regrowth forest is important biodiversity habitat when little mature forest remains. • Identifying regrowth with mature forest elements can guide strategic reservation. • Stand maturity related weakly to remote-sensed and measured environmental variables. • Eucalypt crown senescence weakly indicates stands likely to contain habitat trees. • Timber production and conservation are not in conflict on more productive sites. Abstract In this study, we examined the associations between field-assessed floristic and structural habitat values for mature forest and GIS-derived variables to assess whether high conservation value forests could be predicted for strategic reservation at a landscape scale. We investigated the Eucalyptus regnans forests of the Victorian Central Highlands in south-eastern Australia, where several extensive wildfires in the last century have left little mature forest. We assessed the extent to which the floristic composition and a suite of habitat-related structural variables could be explained by two forest inventory GIS variables (percentage senescence and site productivity) and whether explanatory capacity improved from inclusion of additional environmental variables (climate, soils, topography, structure and spatial location). Results showed that the floristic composition was weakly related to productivity, but not to percentage senescence. Four habitat-related structural variables were positively related to percentage senescence (density of old-growth eucalypts, the quadratic mean diameter (QMD) of both live and dead eucalypts, and the maximum eucalypt form class (a proxy for tree hollows)) while the volume of CWD had a marginally significant positive relationship. Three structural variables were related to productivity (the maximum eucalypt form class, the QMD of dead understorey trees and of dead eucalypts). However, in all cases the explanatory power of percentage senescence and productivity was weak (proportion of deviance explained by the models <0.3). Inclusion of the other environmental variables did not substantially improve explanatory power in any case. Our results suggest that there is a high degree of stochasticity driving floristic and structural composition within these forests, making the detection of most mature forest values difficult without site visits. There may be some limited capacity for the presence of senescent trees visible in aerial photographs to highlight stands more likely to contain habitat trees, but there was no relationship with floristic maturity. Our results also suggest that more productive sites do not have substantially greater habitat values, indicating that the current timber harvesting approach of prioritising the harvest of stands on more productive sites is unlikely to have negative consequences for biodiversity. [ABSTRACT FROM AUTHOR]

Variable retention (VR) is increasingly being used as an alternative to clearcutting in temperate and boreal forests. VR is an approach to harvesting and regeneration that aims to improve biodiversity and social outcomes over the subsequent rotation, while continuing to meet silvicultural and economic imperatives. Aggregated retention, a form of VR in which patches of unharvested forest are retained at harvest, has been used operationally in Tasmania’s public oldgrowth wet eucalypt forests since 2007. Development of aggregated retention required articulation of goals and guidelines for implementation in the Tasmanian context. An extensive research and monitoring program, as well as close liaison between research, management and operational staff, facilitated the adaptive management process. These arrangements aimed to overcome operational challenges and ensure that silvicultural practices were consistent with the available science and expert judgement relating to biodiversity outcomes. The three over-arching ecological objectives for VR silviculture in Tasmania were: Objective 1, facilitating rapid re-establishment of mature forest biodiversity in the harvested area by providing forest influence over the majority of the harvested area; Objective 2, ensuring the retention (2a) and integrity (2b) of biological legacies; and Objective 3, creating favourable conditions for plant regeneration and animal habitat in the harvested area, with connectivity between retained forest edges and the regenerating stand. An individual VR harvest operation (‘coupe’) needed to meet all three objectives in order to receive an overall rating as having delivered the ecological goals of VR. Twelve criteria were then established for assessing attainment of specific aspects of these objectives in each VR coupe, and metrics were developed to score harvest outcomes against each of these criteria. We present the results from 33 coupes that were harvested and regenerated between 2004 and 2010. Coupes harvested early in the development of VR usually rated well against Objectives 1 and 2a, less well against Objective 2b and poorly against Objective 3. Broadcast regeneration burns are integral to successful eucalypt regeneration. However, they can be more challenging to contain within harvested areas in aggregated retention coupes compared to clearcuts, and initially there were unacceptable levels of fire damage to retained trees, while wide firebreaks damaged soils. Changes in coupe design, in firebreaking practices, and in regeneration burning procedures resulted in coupes rating well against all objectives by 2010. The articulation of clearly defined, documented and measurable ecological objectives accompanied by a transparent assessment process was a key component of the adaptive management process that resulted in successful operational implementation of this new silvicultural system. Elements of this approach could be adapted for application in any forest type worldwide. [ABSTRACT FROM AUTHOR]

Insect defoliation of plantation Eucalyptus sp. is a ubiquitous problem, not only in their native Australia but also in many other countries where Australian defoliators have invaded the introduced eucalypt plantations. Although eucalypts are very resilient to defoliation, their growth suffers and reduces the economic benefits of the resource. An artificial defoliation trial investigated the critical factors relating to patterns of insect defoliation that affect the long-term growth of the plantation eucalypt, E. nitens , in Tasmania, Australia. Current season’s adult-phase foliage was removed manually from two- to three-year-old trees to test four factors: severity (50% or 100% of current adult foliage, equivalent to 11% or 25% of total foliage); disbudding following defoliation (with or without disbudding), timing of defoliation (early or late in the summer) and frequency (for one or two consecutive years). Growth parameters of the trees were measured annually for four years after the initial defoliation, and again thirteen years later, before harvest. The most significant factors affecting the growth of the trees were timing and frequency of defoliation; severity of defoliation and disbudding did not have significant effects over the long term. Trees that received either light or heavy defoliation late in the season for two consecutive years were at least 17% smaller in diameter and MAI in diameter was reduced by at least 21% compared to untreated trees over one rotation. This means they would need to be grown for three to four more years to reach the same stand volume as undefoliated trees at harvest. This would have serious cost implications for plantation managers. To prevent these economic losses, an integrated pest management system should focus on protecting eucalypts from defoliation of 50% or more of current season’s adult foliage late in the summer, and in particular, preventing defoliation from occurring in concurrent years. In addition, the continual decline in growth rates of defoliated trees relative to undefoliated trees beyond the initial four years of measurement also suggests that defoliation impacts predicted by models based on short term studies may need to be treated conservatively. [ABSTRACT FROM AUTHOR]

For the management of forest harvesting it is important to understand the processes that impact the re-colonisation of disturbed forests. Edge effects into disturbed forests have been identified as having important impacts on the re-colonisation of both flora and fauna. In a study system located in southern Tasmania, we investigated whether bryophyte colonisation of harvested forests was impacted by edge effects from a standing mature forest (forest influence) and if this effect persisted through time. We tested this by placing transects across a mature/regeneration forest boundary, then recording bryophyte community composition from the ground and coarse woody debris at set distances from the edge. A chronosequence of harvested forest ages (∼7, ∼27 and ∼45 years post harvesting) was used to determine if forest influence persisted through time. Models generated by non-linear canonical analysis of principal coordinates (NCAP) predicted the depth of forest influence, and ‘distances among centroids’ inferred the magnitude of forest influence. Results showed that bryophyte composition in regeneration forests responded to distance from a mature edge. Locations closer to a mature edge had greater similarity in community composition with mature forests. This study also showed that the response of bryophytes to forests influence persisted though time, even after canopy closure. Overall, mature forest species tended to be aided and early seral species restricted by forest influence. However, responses were species-specific and varied with forest age. The colonisation success of mature forest associated species was improved by forest influence; these species are typically at most at risk of being eliminated after disturbance. This result highlights the need to consider edge effects in management. The impact of forest influence on bryophytes therefore has the potential to be used in the design of areas to be harvested. [ABSTRACT FROM AUTHOR]

Optimising design and implementation of reserve networks in production forests is paramount in ensuring successful and sustainable management of forests. Riparian reserves are common requirements of forest practices legislation around the world. However, many reserve allocations, including those present in Tasmanian wet eucalypt production forests, are biased towards streamside reservations with less representation of upslope non-riparian habitat. This study aimed to determine whether this trend is leading to a conservation bias for those species sensitive to microclimatic differences between streamside and upslope habitat, such as bryophytes. We therefore used a paired sample approach to compare bryophyte communities growing on logs within streamside areas to communities 100 m upslope. Results showed that species richness was significantly greater in the streamside areas, although overall community composition did not significantly differ. While 30% of species occurred exclusively in streamside habitat, no species were found only in upslope habitat, and nestedness analysis indicated that, for most sites, upslope communities were nested within those of the nearby streamside communities. Therefore, in terms of species conservation, it appears that at least for wet forest log-associated bryophytes, there is no need to modify current reserve designs to protect upslope habitat. [ABSTRACT FROM AUTHOR]

Microclimatic forest influence (edge effects into open or regenerating areas) occurs within harvested forest, but the depth and magnitude may change depending on the design of the harvested area. This is an important consideration for managers, because gradients in microclimate can significant affect the ability of species to recolonise following disturbance. One harvesting method that can increase the amount of forest influence is aggregated retention. This technique involves leaving groups of trees (aggregates) within the harvested area, thus increasing the amount of regenerating forest that is near to an edge and therefore under forest influence. However, differences in the scale of forest influence generated from aggregates compared to unlogged forests surrounding harvested areas have not been tested. Understanding the ability of retained aggregates to generate forest influence is important in designing and implementing aggregated retention harvesting practices. This study tested whether retained aggregates generated similar levels of forest influence as mature forest surrounding harvested areas. Microclimatic forest influence was examined by monitoring spatial changes in air temperature and relative humidity along transects running from within standing mature forest into harvested forest. Intact forest and aggregate transects were located in the direction of maximum expected forest influence (south-facing edges). Results showed that forest influence was mostly similar in both depth and magnitude regardless of the type of forest from which it was generated. Temporal examination of forest influence showed that it changed throughout the day and across the year, with peaks in magnitude occurring during the middle of the day, and in months close to the equinoxes. Shade derived from standing trees was a potential driver of temporal patterns in microclimatic forest influence. At its peak magnitude, the microclimatic forest influence observed will likely have significant impacts on habitat suitability and thus, presumably, species recolonisation after disturbance. Results indicated that aggregated retention is an effective method for generating forest influence within harvested areas. Therefore, aggregated retention has the potential to be a valuable harvesting technique to alter microclimate and have beneficial impacts on the recovery of harvested forests. [ABSTRACT FROM AUTHOR]

Aggregated retention, in which patches of trees (aggregates) remain unlogged within larger harvested units, was first applied commercially in 1986. A primary goal was to maintain greater diversity of forest-dependent species through harvest, relative to conventional clearcutting. Despite its global application, the long-term benefits for biodiversity and the comparative responses of disparate taxonomic groups to aggregated retention are largely unknown. A critical knowledge gap relates to the role of ‘forest influence’ – whether and to what extent aggregates affect biodiversity in neighboring harvested areas. We sampled plants, beetles, and spiders/harvestmen in the world’s three oldest aggregated-retention sites (21–26 years old), matched with three recently harvested sites (5–8 years old). For each taxonomic group, we compared species composition between undisturbed aggregates and regenerating forests to assess the ‘lifeboating’ function of aggregates. For each group, we also modeled changes in species composition, and in the numbers of aggregate- and regeneration-affiliated species, with distance from the aggregate edge into the regenerating forest along transects at north-facing edges. For all three taxa, species composition differed between aggregates and regenerating forests in both older and recent sites, confirming the long-term effectiveness of aggregates for lifeboating. The compositional difference between habitats was significantly greater at recent than at older sites for plants, but not for invertebrates. Plants and spiders/harvestmen responded to forest influence, with a marginal response for beetles. Responses for plants and spiders generally manifested as increased numbers of aggregate-affiliated species and decreased numbers of regeneration-affiliated species in regenerating areas closer to edges. Our results indicate that aggregated retention has short- and long-term benefits for biodiversity reflecting both the lifeboating and forest-influence functions of aggregates. However, variation in the responses of plants, beetles and spiders suggests that these benefits cannot be generalized among taxa. We advocate broader application of aggregated retention in forests managed for timber production and encourage managers to incorporate the benefits of forest influence in harvest designs by arranging aggregates to reduce average distances from harvested areas to unlogged habitats. [ABSTRACT FROM AUTHOR]

• Soil seed banks of wet temperate forests provide a storage effect. • Fire-cued germination concentrated in ant-dispersed species. • Germination of shade-tolerant species not enhanced by fire cues. • Edaphic variability and structural complexity promote plant diversity. • Practices that generate heterogenous environments will benefit biodiversity. Our understanding of how environmental heterogeneity shapes plant community dynamics is largely based on above-ground diversity despite the importance of seed banks as reservoirs of genetic and taxonomic diversity that buffer plant populations and influence vegetation following disturbance. Using a plant functional trait approach, this study examined the importance of fire-related germination cues and environmental determinants of plant community turnover in wet forests of south-eastern Australia – forests of both high conservation value and the focus of current timber harvesting. We surveyed extant vegetation, soil seed banks, forest structure and edaphic properties across 62 sites burnt in 1939 and not subsequently affected by wildfire or logging. A total of 46 families, and 99 species were identified in extant vegetation with 43 and 126 respectively in the soil seed bank, with only 32% of species co-occurring in both species' pools. Despite historically long fire return intervals, the soil seed bank demonstrated a clear positive response to fire-related germination cues (heat in combination with smoke) that were concentrated in hard-seeded species dispersed by ants. Seeds from early successional species showed no response to fire cues, while species typical of the wetter margins of these forests were killed by high heat. The soil seed bank was dominated by species associated with early successional stages, consistent with the initial floristics model of succession. Woody species were largely restricted to extant vegetation and replacement is most likely to occur from future seed rain. Spatially structured environmental heterogeneity shaped plant turnover with the relative strength of environmental controls differing among functional types and pools of diversity. Differential response of the combined species pool relative to extant vegetation demonstrates that the soil seed bank provides a storage effect. Forest management practices that generate patchy and heterogenous environments, including the intensity of regeneration burns and density of overstorey species, will benefit biodiversity conservation through overstorey structural controls on resource availability and diversity of understorey vegetation, that is transferred to soil seed banks via tight abiotic controls and seed inputs. [ABSTRACT FROM AUTHOR]

A major aim of sustainable forest management is the maintenance or recolonisation of harvested areas by species that were present pre-disturbance. Forest influence (a type of edge effect that focuses on the effect of mature forests on adjacent disturbed forest) is considered to be an important factor that contributes to the ability of mature forest species to re-colonise disturbed areas. Forest influence occurs in two main ways by: (1) by providing a source of propagules or individuals for recolonisation; and (2) by its influence on the biotic and abiotic conditions of the disturbed forest. This study focuses on forest influence’s impact on microclimate conditions of adjacent disturbed areas regenerating after harvesting. In particular, the study investigates whether microclimate within a regenerating forest changes with increasing distance from a mature forest edge, and whether the magnitude of microclimatic change varies over diurnal, seasonal and successional time scales. Results of the study showed that the microclimate of regenerating forests is affected by the distance to a standing mature forest. Temperature, relative humidity, vapour pressure deficit, and the short-term fluctuations of these microclimate parameters were influenced by nearby mature forest. In addition, the study found that the magnitude of forest influence changes over diurnal, seasonal and successional time scales. For example, it was discovered that forest influence is greatest during the middle of the day, during the summer months when solar heating is greatest and on hot windy days. Critically, the impact of forest influence peaked around ∼27 years after disturbance in the areas studied, with less influence shortly after disturbance. We speculate this is due to lower levels of midday shading in the ∼7 year old forest. Forest influence on microclimate persisted in regeneration areas that were harvested 45 years ago, although the magnitude and importance of the effect was low. We conclude that proximity to mature forest stands (forests influence) impacts the microclimate of forests regenerating after disturbance, although the response is quite variable through time. Our results provide insight into the role of microclimate on the ability of mature forest species to successfully re-colonise after disturbance. Management practices, such as aggregated retention and other forms of retention forestry, which increase the proportion of harvested area under forest influence, may provide a mechanism to promote the re-colonisation of mature-forest species. [ABSTRACT FROM AUTHOR]

Highlights: [•] Pre-harvest vegetation strongly affects post-harvest composition. [•] Vegetation in wildfire-disturbed forest is similar to that in harvested forest. [•] Coppice regeneration is less common in harvested than wildfire-burnt forest. [•] Aggregates as seed sources are not influencing initial plant establishment. [ABSTRACT FROM AUTHOR]

Highlights: [•] Mature forest proximity affects re-establishment of biodiversity after logging. [•] All biodiversity groups are affected, but scales and mechanisms vary. [•] Scale of re-establishment varies with dispersal capacity and habitat gradients. [•] Height of retained forest is rarely directly scaled to distance of re-establishment. [•] Harvest layouts should promote mature forest proximity to functional refugia. [ABSTRACT FROM AUTHOR]

Abstract: In Tasmania, Australia, aggregated retention (ARN [1] Abbreviations: ARN, aggregated retention; CBS, clearfell, burn and sow. 1 ) is being implemented as an alternative to clearfelling in old-growth wet eucalypt forests. These forests have traditionally been regenerated using a high-intensity burn and aerial sowing, but the use of more complex harvesting designs makes conventional high-intensity burning difficult. In 2007, a new burning method (‘slow burning’) was developed specifically for ARN coupes. This paper compares site preparation, burning weather conditions and burning outcomes in ARN and conventional clearfell, burn and sow (CBS) coupes burnt from 2007 to 2010. ARN coupes had higher perimeter-to-area ratios than paired CBS coupes, and 8% more of the harvested area was affected by firebreaks. Although there was less burnt seedbed and more compacted seedbed in ARN coupes compared to clearfelled coupes, mean levels of receptive seedbed were adequate and are unlikely to limit regeneration success. Burn impact on unharvested forest was greater in ARN coupes, due largely to burning in the retained aggregates. Despite this, only 11% of aggregate area was burnt overall, and the current guidelines for aggregate size (most >1ha) appear sufficient to keep burn impact within acceptable thresholds. Firebreaks affected from 4–32% of the harvested area in the coupes measured in this study, and were 10m wide on average, twice the required width. To reduce soil disturbance and potential impacts on regeneration, firebreaks should be established only where absolutely necessary, and firebreak widths should be minimised wherever possible. [Copyright &y& Elsevier]

Abstract: Aggregated retention (a type of variable retention) is a silvicultural practice that is being implemented in forests worldwide as an alternative to traditional clearfelling (clearcutting) practices. Aggregated retention retains patches of unlogged forest within the harvested matrix. It has been proposed that it retains biodiversity values better than clearfelling, although, to date, there has been limited research on small mammal responses to this practice, especially in southern hemisphere systems. This study determined whether aggregated retention provided a “lifeboat” for two native rodent species; the habitat specialist, cover-dependent swamp rat (Rattus lutreolus velutinus), and the habitat generalist, long-tailed mouse (Pseudomys higginsi), in wet Eucalyptus forests. We compared their abundances in three forestry treatments (clearfell, burn and sow, unlogged native forest and aggregated retention (including edges, islands and harvested matrix)) over three trapping periods (one- to three-years post-burn), and assessed the effect of habitat cover (vegetation) on rodent abundances. The cover-dependent swamp rat was found in highest abundance in unlogged forest, intermediate in aggregated retention and lowest in clearfelling. Within aggregated retention, there was a trend for decreasing swamp rat abundance with increasing disturbance within the different habitat types (highest abundance in edges, intermediate in islands, lowest in harvested matrix). The generalist long-tailed mouse, was found in equal abundance across all forestry treatments and habitat types. Island size within aggregated retention coupes had no effect on the presence of either species. Sex ratios did not differ between forestry treatments or habitat types for either species, although swamp rats showed female dominance irrespective of treatment or habitat type. Within harvested areas, a high percentage understorey cover was an important predictor of swamp rat abundance. Our results demonstrate that aggregated retention provides a lifeboat for cover-dependent small mammals in comparison to traditional clearfelling practices. The habitat cover provided by the retained forest allows populations to persist in connected and isolated patches within production landscapes. Vegetation density at the lower strata appears to be an important determinant for recolonisation in harvested areas. [Copyright &y& Elsevier]

Abstract: The Warra Silvicultural Systems Trial (SST) in Tasmania, Australia provides a framework for investigating the responses of beetles (Order: Coleoptera) to three alternative systems in lowland wet eucalypt forest: aggregated retention; dispersed retention; and understorey islands retained in clearfelled areas. Beetles from three families known to be sensitive to forest management, the families Carabidae (ground-beetles), Curculionidae (weevils) and Leiodidae (fungus-beetles), were collected with pitfall traps prior to harvest, and in the first and third years post-harvest. The retained aggregates in the aggregated retention system maintained beetle assemblages reasonably typical of mature forests, at least in these early years following harvesting. These aggregates appear to provide a stable habitat, with similar species composition in the first and third years post-harvest. In contrast, the harvested areas of the aggregated retention system contained low numbers of beetle species affiliated with mature forest, as did the understorey islands and the dispersed retention system. Relative to clearfelling, all alternative silvicultural systems appeared to be of some benefit to beetles affiliated with mature forest, but aggregated retention retained far greater numbers of these beetles compared to the other systems in Tasmanian wet eucalypt forest. [Copyright &y& Elsevier]

• Bacterial communities in burnt soils recover lost abundance and diversity over time. • Logging and burn impacts on fungal abundance and diversity persist. • Both beneficial and antagonistic microbes negatively impacted by burning. • A range of burn severities help promote diverse soil communities post-logging. Globally, forest ecosystems are increasingly impacted by natural and anthropogenic disturbances including fire, timber harvesting and land clearance. Understanding how soil bacteria and fungi are impacted by logging and burning is important for resource management, as these microbiota underpin many essential ecosystem processes such as nutrient cycling and soil formation. Using amplicon sequencing and qPCR of the bacterial 16S rRNA gene and fungal ITS1 region, we quantified the abundance, diversity, and composition of soil bacterial and fungal communities in undisturbed forest and adjacent logged and burnt sites, which included a mosaic of burning severities (unburnt, low severity and high severity burns). Our study was conducted over a 12-month time series post-burn, in the temperate wet eucalypt forests of Tasmania, Australia. We found that over this 12-month period i) after high severity burns, total abundance and diversity returned to pre-disturbance levels in bacterial communities but not in fungal communities and ii) for each disturbance severity, the composition of bacterial communities became more similar to the undisturbed reference communities over time, while fungal communities did not. We also characterised the succession of disturbance responsive taxa in logged and burnt communities, with the relative dominance of copiotrophic bacteria and fire-associated Ascomycota fungi shifting towards oligotrophic bacteria and fire-associated Basidiomycota fungi by 12-months. Further, we highlight specific taxa that respond positively or negatively to the impacts of fire disturbance and discuss the ecological implications of our findings for forest management. [ABSTRACT FROM AUTHOR]

Abstract: Edge effects potentially have negative consequences for biodiversity in logging areas. In Tasmanian wet eucalypt forest, ground-dwelling beetle assemblages responded to habitat edges between mature unlogged forest and young regeneration following clearfelling. Transects of pitfall traps extended 100m into unlogged forest and 10m into the felled area firebreaks at four study sites (4 sites×3 transects×8traps/transect=96traps). The depth of edge influence extended between 10m and 25m into mature forest, and the beetle assemblage was estimated to be 95% similar to interior forest at approximately 22m from the edge. The species composition of beetles changed gradually with distance from the edge, but for practical purposes we distinguished three zones of edge response: mature forest interior extending ≥22m into unlogged forest, firebreak habitat at the edge of the coupe that extends 1m into unlogged forest, and an edge-affected mature forest zone in between. Individual species known to be characteristic of mature and young forest were of greatest indicator value in mature forest interior and firebreak habitat, respectively. Choleva TFIC sp 01 (Leiodidae), Decilaus nigronotatus, D. lateralis and D. striatus (all Curculionidae) were identified as indicator species characteristic of mature forest interior. No species were found to be characteristic of the habitat edges. These results are relevant to current management practices in Tasmanian wet eucalypt forest, in particular to the efficacy of linear reserve networks. One hundred metre wide wildlife habitat strips, when bounded by recently harvested forest, are estimated to contain a little over 50% of interior habitat not compromised by edge effects. Small patches of forest (<1ha) retained in variable retention harvesting are predicted to contain little or no uncompromised interior habitat for ground-dwelling beetles. [Copyright &y& Elsevier]

Abstract: Reserve corridors in production forestry landscapes are frequently concentrated in riparian areas. This study describes the numerical response of ground-dwelling beetles to increasing distance from streams, with the aim of evaluating the effectiveness of such a bias in reserve allocation. Patterns in abundance and diversity of epigaeic beetles were quantified at four first order streams in wet eucalypt forest in Tasmania, Australia. The depth and pattern of beetles’ riparian response varied between streams. Commonly trapped beetles were less abundant near to three of the four streams, and the numerical response model differed in each case. Species richness of common beetles was also lower near one of the streams. Pooled abundance and richness of rare species did not vary in response to the riparian–upslope transition. No riparian or upslope specialist species were identified among the most commonly collected species. Compared to upslope habitat, the riparian–upslope transition encompassed greater variability in species composition without actually increasing overall richness. The study findings demonstrate the need for ecosystem-specific data to optimize reserve placement, since the results were not predicted from general vegetation patterns, ecological theory, or the widely held assumption that riparian areas support greater abundance and diversity of organisms than adjacent upslope areas. Reserves encompassing more upslope habitat are recommended to complement those located in riparian areas. [Copyright &y& Elsevier]

The ecological effects of clearfell harvesting followed by high intensity burning are sometimes thought to mimic wildfire, the major natural disturbance regime in Tasmanian wet forests. We investigated whether the litter-inhabiting beetle populations in logged and burnt regeneration forest resembled those in forest regenerating following natural wildfire. Pitfall trapping and habitat assessment were conducted at three pairs of adjacent 33-year-old logging and wildfire regeneration sites. In total, 6128 beetles were collected, representing 179 morphospecies in 30 families. The beetle assemblages in logging and wildfire treatments could not be distinguished. However, beetle populations did differ subtly between sites. One Aleocharinae (Staphylinidae) morphospecies and one Carabidae species were more abundant at one of the three site pairs. Multivariate analyses of common species indicated that the litter beetle assemblages differed significantly between sites, and this was partially related to their degree of geographical separation. Environmental factors considered indicative of logging impacts did not differ between wildfire and logging regeneration treatments.Temporal and landscape scale differences between logging and the natural disturbance regime and changes to logging practices since these study sites were harvested may have negative impacts on litter beetles in the future. Changes to current harvesting practices are recommended to better mimic the natural disturbance regime and thus improve conservation of forest biodiversity. [Copyright &y& Elsevier]

The value of diversity metrics to represent ecological communities and inform broad-scale conservation objectives and policy has often been subject to debate and uncertainty [1,2] . In practice, diversity metrics are important in setting management and conservation priorities, just as economic indices contribute to global monetary and financial policies. Thus, key challenges for ecologists are to identify new ways to view and summarise patterns in biodiversity and improve on the metrics available for management purposes. In a recent paper on functional diversity patterns in reef fishes [3] , we highlighted the potential of new insights gained from functional trait-based approaches to inform marine management, stressing the need to develop and refine biodiversity measures that are linked to ecology (rather than taxonomy). We used a unique, fisheries-independent reef fish identity and abundance dataset, collected using standardised methods from equatorial to high latitude regions all over the world, to provide the first global view of the distribution of individuals amongst species (including a measure of evenness) and functional traits amongst marine communities. A recent paper by Robinson et al. [4] published in Marine Policy criticised the use of our evenness index as a measure of biodiversity, and questioned the use of functional trait-based metrics derived from surveys of standardised areas for decisions relating to broad-scale management of marine systems. In this paper we respond to Robinson et al. and rebut their claims related to sampling bias and broad-scale applicability of trait-based approaches. [ABSTRACT FROM AUTHOR]

• Beetle communities in regeneration forests were mostly driven by spatial factors. • Beetle communities were not fully recovered by ~50 years after harvesting. • High amount of mature forests in the nearby landscape facilitated beetle recovery. • Proximity to mature forest was less influential than amount of mature forests. Landscape conservation planning in managed forests requires information on the relative importance of different aspects of mature forests. Regeneration forest sites with greater access to source populations for re-establishment of biodiversity are expected to have greater similarity in species composition to unharvested mature areas, i.e., when sites are in close proximity to mature forest (forest influence), and/or have a high percentage of mature forest in the surrounding landscape (landscape context). We investigated how recovery of ground-active beetle biodiversity in the mid-late successional stage (40–58 years) of previously harvested regeneration forests is affected by forest influence, landscape context, and other characteristics of the surrounding landscape. We used DNA metabarcoding to characterise beetle communities in 12 mature forest sites and 64 regeneration forest sites. Generalized dissimilarity modelling (GDM), constrained redundancy analysis, and ordinations evaluated the contribution of predictors (i.e., bioclimate, landscape configuration, regeneration age, spatial position and topography) to beetle composition. Beetle composition was significantly different between different forest ages and landscape context classes. GDM of all predictors explained 34.1% of total variance in beetle community turnover. While the geographic locations of sites accounted for most (75.1%) of composite ecological gradients, the beetle community is subtly influenced by the effects of landscape context (1.8%), forest influence (1.2%) and other variables relating to landscape configuration (collectively 5.2%). Long-term conservation of local biodiversity in managed forests requires maintaining a certain amount of mature forest, but their importance as beetle source populations declines as the regeneration forests mature. [ABSTRACT FROM AUTHOR]

• Large, old trees with hollows provide important habitat for hollow-using species. • Retention forestry can help retain habitat trees in harvested areas. • Aggregated retention retained more habitat trees than other silvicultural systems. • Aerial and ground-based surveys gave similar estimates of habitat tree abundance. • Helicopter surveys are a rapid, cost-effective approach for post-harvest assessment. Habitat trees (mature live and dead trees with hollows) are a keystone habitat in Australian eucalypt forests where tree hollows typically occur in large, old trees. These trees provide potential habitat for hollow-using birds, bats and arboreal marsupials, including many threatened species. Habitat trees may be felled during forest harvesting and can also be negatively affected by wildfires. Shortages of habitat trees in harvesting landscapes can be a limiting factor for populations of hollow-using vertebrates. Retention forestry systems are expected to retain a greater number of habitat trees within sites than traditional clearcutting silviculture, but there is a need to quantify how the pattern of retention (dispersed trees vs. retained clumps) will affect the numbers and types of trees retained. The method of assessment (ground-based vs. aerial surveys) may influence the estimated numbers of habitat trees. We investigated habitat tree retention at the Warra Silvicultural Systems Trial in Southern Tasmania, Australia. This trial was instrumental in developing alternatives to clearcutting in tall, wet, old-growth eucalypt forests. Our research has two objectives. Objective 1 is to assess the numbers of habitat trees retained in various alternatives to clearcutting by comparing: unlogged control areas, 0.5–1 ha clumps retained within a harvested matrix (aggregated retention), trees scattered throughout the harvested area (dispersed retention), and small ~0.08 ha machinery exclusion zones where trees were retained if they were not of commercial value (clearcutting with understorey islands). Objective 2 is to compare ground-based to aerial, helicopter-based, assessment of large live and dead trees. Although low replication of harvest treatments precluded statistical comparison of silvicultural systems, the results, based on 1,260 trees, were clear. Of the various alternatives to clearcutting, aggregated retention retained the greatest proportion of all classes of habitat trees, primarily because of higher retention targets, but possibly also because of greater survival with reduced wind exposure in aggregates. Substantially fewer habitat trees were retained with dispersed retention, and virtually none with understorey islands in clearcutting. Aerial and ground-based assessment methods provided similar estimates of numbers of trees with visible hollows in aggregates and understorey islands (R2 = 0.95). Choice of method for future studies should consider available resources and objectives, since there were advantages and disadvantages of each approach. In conclusion, aggregated retention was found to be the preferred silvicultural system for retaining habitat trees within sites for hollow-using vertebrates, and helicopter surveys provide a rapid alternative to traditional ground-based assessment. [ABSTRACT FROM AUTHOR]

Reef Life Survey (RLS) provides a new model for ecological monitoring through training experienced recreational divers in underwater visual census methods to the level of skilled scientists. Detail produced is similar to that of programs with professional scientific teams, at low cost to allow global coverage. RLS differs from most other citizen science initiatives in its emphasis on rigorous training and data quality rather than open participation, selectively involving the most skilled and committed members. Volunteers participate primarily because they appreciate the close relationship with scientists, other divers, and managers, and see their efforts directly contributing to improved environmental outcomes. RLS works closely with Australian management agencies, scheduling annual events at core monitoring sites associated with 10 inshore marine protected areas Australia-wide. Surveys of 12 offshore Australian Marine Parks (AMPs) are realized through 2–4 week voyages in a sailing catamaran crewed by volunteers. Across the AMP network, RLS surveys have quantified densities of fishes, mobile invertebrates, macroalgae and corals at 350 shallow coral reef sites (180 sites surveyed on two or more occasions), providing an understanding of (i) population changes amongst threatened species including sea snakes, (ii) responses of fish and invertebrate populations following fisheries closures, (iii) ecosystem-wide impacts of marine heat-waves, and (iv) the extent that AMPs spanning the network comprehensively encompass national coral reef biodiversity. This scientist/volunteer/manager collaboration could be greatly expanded globally (presently 3537 sites in 53 countries). • Global monitoring of reef communities using standardized visual census methods • Divers assess densities of fishes, reptiles, mobile and sessile invertebrates, and macro-algae • Involves collaboration of highly trained volunteer divers, researchers and managers • Data now collected from 3537 sites in 53 countries • Management agencies use data to assess effects of fishing, climate change and pollution [ABSTRACT FROM AUTHOR]

Murine hepatitis virus (MHV) has long served as a model system for the study of coronaviruses. Non-structural protein 3 (nsp3) is the largest nsp in the coronavirus genome, and it contains multiple functional domains that are required for coronavirus replication. Despite the numerous functional studies on MHV and its nsp3 domain, the structure of only one domain in nsp3, the small ubiquitin-like domain 1 (Ubl1), has been determined. We report here the x-ray structure of three tandemly linked domains of MHV nsp3, including the papain-like protease 2 (PLP2) catalytic domain, the ubiquitin-like domain 2 (Ubl2), and a third domain that we call the DPUP (domain preceding Ubl2 and PLP2) domain. DPUP has close structural similarity to the severe acute respiratory syndrome coronavirus unique domain C (SUD-C), suggesting that this domain may not be unique to the severe acute respiratory syndrome coronavirus. The PLP2 catalytic domain was found to have both deubiquitinating and deISGylating isopeptidase activities in addition to proteolytic activity. A computationally derived model of MHV PLP2 bound to ubiquitin was generated, and the potential interactions between ubiquitin and PLP2 were probed by site-directed mutagenesis. These studies extend substantially our structural knowledge of MHV nsp3, providing a platform for further investigation of the role of nsp3 domains in MHV viral replication. [ABSTRACT FROM AUTHOR]

Abstract: Design, synthesis and biological evaluation of a series of 5-chloropyridine ester-derived severe acute respiratory syndrome-coronavirus chymotrypsin-like protease inhibitors is described. Position of the carboxylate functionality is critical to potency. Inhibitor 10 with a 5-chloropyridinyl ester at position 4 of the indole ring is the most potent inhibitor with a SARS-CoV 3CLpro IC50 value of 30nM and an antiviral EC50 value of 6.9μM. Molecular docking studies have provided possible binding modes of these inhibitors. [Copyright &y& Elsevier]

Severe acute respiratory syndrome coronavirus (SARS-CoV) is a novel coronavirus that causes a highly contagious respiratory disease, SARS, with significant mortality. Although factors contributing to the highly pathogenic nature of SARS-CoV remain poorly understood, it has been reported that SARS-CoV infection does not induce type I interferons (IFNs) in cell culture. However, it is uncertain whether SARS-CoV evades host detection or has evolved mechanisms to counteract innate host defenses. We show here that infection of SARS-CoV triggers a weak IFN response in cultured human lung/bronchial epithelial cells without inducing the phosphorylation of IFN-regulatory factor 3 (IRF-3), a latent cellular transcription factor that is pivotal for type I IFN synthesis. Furthermore, SARS-CoV infection blocked the induction of IFN antiviral activity and the up-regulation of protein expression of a subset of IFN-stimulated genes triggered by double-stranded RNA or an unrelated paramyxovirus. In searching for a SARS-CoV protein capable of counteracting innate immunity, we identified the papain-like protease (PLpro) domain as a potent IFN antagonist. The inhibition of the IFN response does not require the protease activity of PLpro. Rather, PLpro interacts with IRF-3 and inhibits the phosphorylation and nuclear translocation of IRF-3, thereby disrupting the activation of type I IFN responses through either Toll-like receptor 3 or retinoic acid-inducible gene I/melanoma differentiation-associated gene 5 pathways. Our data suggest that regulation of IRF-3-dependent innate antiviral defenses by PLpro may contribute to the establishment of SARS-CoV infection. [ABSTRACT FROM AUTHOR]

Abstract: Structure-based design, synthesis, and biological evaluation of a series of peptidomimetic severe acute respiratory syndrome-coronavirus chymotrypsin-like protease inhibitors are described. These inhibitors were designed and synthesized based upon our X-ray crystal structure of inhibitor 1 bound to SARS-CoV 3CLpro. Incorporation of Boc-Ser as the P4-ligand resulted in enhanced SARS-CoV 3CLpro inhibitory activity. Structural analysis of the inhibitor-bound X-ray structure revealed high binding affinity toward the enzyme. [Copyright &y& Elsevier]