Long‐term mammal and nocturnal bird trends are influenced by vegetation type,weather and climate in temperate woodlands

Many studies have documented the individual effects of variables such as vegetation, long‐term climate and short‐term weather on biodiversity. Few, however, have explicitly explored how interactions among these major drivers can influence species abundance. We used data from a 15‐year study (2002–2017) in the endangered temperate woodlands of south‐eastern Australia to test hypotheses associated with the effects of vegetation type, long‐term climate and short‐term weather on population trajectories of seven species of (largely) nocturnal mammals and birds. Despite prolonged drought conditions, there was a significant increase in the abundance of some species over time (e.g. the Eastern Grey Kangaroo). It is possible that destocking of domestic livestock may have reduced competition with Kangaroos, thereby facilitating increases in abundance. The Common Brushtail Possum and Common Ringtail Possum were significantly less likely to occur in replanted woodlands, possibly because of the paucity of nesting sites. We found no evidence that replanted woodlands are refuges for exotic pest species like the European Rabbit and Red Fox. Short‐ and long‐term rainfall and vegetation type had important independent and combined effects on animal abundance. That is, responses to periods of high short‐term rainfall were dependent on vegetation type and whether sites occurred in long‐term climatically wet versus climatically dry locations. For example, the Red Fox responded positively to high levels of short‐term rainfall, but only at climatically dry sites. Our results highlight the complementary value of different vegetation types across the landscape and the context‐specific responses of animals to short‐term fluctuations in moisture availability. They also underscore the value of long‐term monitoring at a landscape scale for examining how multiple interacting factors influence trends in animal abundance.     

The evolution of realized niches within freshwater Synechococcus

Understanding how ecological traits have changed over evolutionary time is a fundamental question in biology. Specifically, the extent to which more closely related organisms share similar ecological preferences due to phylogenetic conservation – or if they are forced apart by competition – is still debated. Here, we explored the co-occurrence patterns of freshwater cyanobacteria at the sub-genus level to investigate whether more closely related taxa share more similar niches and to what extent these niches were defined by abiotic or biotic variables. We used deep 16S rRNA gene amplicon sequencing and measured several abiotic environmental parameters (nutrients, temperature, etc.) in water samples collected over time and space in Furnas Reservoir, Brazil. We found that relatively more closely related Synechococcus (in the continuous range of 93%–100% nucleotide identity in 16S) had an increased tendency to co-occur with one another (i.e. had similar realized niches). This tendency could not be easily explained by shared preferences for measured abiotic niche dimensions. Thus, commonly measured abiotic parameters might not be sufficient to characterize, nor to predict community assembly or dynamics. Rather, co-occurrence between Synechococcus and the surrounding community (whether or not they represent true biological interactions) may be a more sensitive measure of realized niches. Overall, our results suggest that realized niches are phylogenetically conserved, at least at the sub-genus level and at the resolution of the 16S marker. Determining how these results generalize to other genera and at finer genetic resolution merits further investigation.     

Soil and root nutrient chemistry structure root-associated fungal assemblages in temperate forests

Root-associated fungi (RAF) link nutrient fluxes between soil and roots and thus play important roles in ecosystem functioning. To enhance our understanding of the factors that control RAF, we fitted statistical models to explain variation in RAF community structure using data from 150 temperate forest sites covering a broad range of environmental conditions and chemical root traits. We found that variation in RAF communities was related to both root traits (e.g., cations, carbohydrates, NO₃⁻) and soil properties (pH, cations, moisture, C/N). The identified drivers were the combined result of distinct response patterns of fungal taxa (determined at the rank of orders) to biotic and abiotic factors. Our results support that RAF community variation is related to evolutionary adaptedness of fungal lineages and consequently, drivers of RAF communities are context-dependent.     

The importance of naturally attenuated SARS-CoV-2in the fight against COVID-19

The current SARS-CoV-2 pandemic is wreaking havoc throughout the world and has rapidly become a global health emergency. A central question concerning COVID-19 is why some individuals become sick and others not. Many have pointed already at variation in risk factors between individuals. However, the variable outcome of SARS-CoV-2 infections may, at least in part, be due also to differences between the viral subspecies with which individuals are infected. A more pertinent question is how we are to overcome the current pandemic. A vaccine against SARS-CoV-2 would offer significant relief, although vaccine developers have warned that design, testing and production of vaccines may take a year if not longer. Vaccines are based on a handful of different designs (i), but the earliest vaccines were based on the live, attenuated virus. As has been the case for other viruses during earlier pandemics, SARS-CoV-2 will mutate and may naturally attenuate over time (ii). What makes the current pandemic unique is that, thanks to state-of-the-art nucleic acid sequencing technologies, we can follow in detail how SARS-CoV-2 evolves while it spreads. We argue that knowledge of naturally emerging attenuated SARS-CoV-2 variants across the globe should be of key interest in our fight against the pandemic.     

The ecology of chronic wasting disease in wildlife

Prions are misfolded infectious proteins responsible for a group of fatal neurodegenerative diseases termed transmissible spongiform encephalopathy or prion diseases. Chronic Wasting Disease (CWD) is the prion disease with the highest spillover potential, affecting at least seven Cervidae (deer) species. The zoonotic potential of CWD is inconclusive and cannot be ruled out. A risk of infection for other domestic and wildlife species is also plausible. Here, we review the current status of the knowledge with respect to CWD ecology in wildlife. Our current understanding of the geographic distribution of CWD lacks spatial and temporal detail, does not consider the biogeography of infectious diseases, and is largely biased by sampling based on hunters' cooperation and funding available for each region. Limitations of the methods used for data collection suggest that the extent and prevalence of CWD in wildlife is underestimated. If the zoonotic potential of CWD is confirmed in the short term, as suggested by recent results obtained in experimental animal models, there will be limited accurate epidemiological data to inform public health. Research gaps in CWD prion ecology include the need to identify specific biological characteristics of potential CWD reservoir species that better explain susceptibility to spillover, landscape and climate configurations that are suitable for CWD transmission, and the magnitude of sampling bias in our current understanding of CWD distribution and risk. Addressing these research gaps will help anticipate novel areas and species where CWD spillover is expected, which will inform control strategies. From an ecological perspective, control strategies could include assessing restoration of natural predators of CWD reservoirs, ultrasensitive CWD detection in biotic and abiotic reservoirs, and deer density and landscape modification to reduce CWD spread and prevalence.     

Fungal functional ecology: bringing a trait‐based approach to plant‐associated fungi

Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro‐organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function . Trait‐based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and ‐omics‐based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (Fun^Fun). Fun^Fun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait‐based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.     

A critical evaluation of the Oscillayers methods and datasets

Here we evaluate Oscillayers, a new method that aims to estimate palaeoclimates for the past 5.4 Myr, and discuss the associated theoretical and methodological issues. We show that the theoretical foundation of Oscillayers is inherently limited, because the method cannot incorporate spatio‐temporal variation and different forcing mechanisms into climate reconstructions. In addition, several methodological weaknesses are clarified that entrench the palaeoclimatic reconstruction of Oscillayers to patterns of climate change observed between the Last Glacial Maximum and current climates. We test the utility of the Oscillayers method to produce palaeoclimatic reconstructions that are similar to general circulation model (GCM)‐based estimates. On average, only 55.6% of values in the mean annual temperature datasets across the Pliocene and Pleistocene were within ±3°C when compared with corresponding GCM‐based datasets. Furthermore, on average only 75.3% of values in the mean annual precipitation datasets across the Pliocene and Pleistocene were within ±200 mm of rainfall of the GCM‐based estimates. Our results demonstrate that the Oscillayers approach does not provide a robust approximation of palaeoclimatic conditions throughout the Plio‐Pleistocene. Thus, when these datasets are used for scientific analyses, the results should be interpreted with a full appreciation of their limitations, particularly for periods outside the last glacial cycle.     

Exposure to noise pollution across North American passerines supports the noise filter hypothesis

The noise filter hypothesis predicts that species using higher sound frequencies should be more tolerant of noise pollution, because anthropogenic noise is more intense at low frequencies. Recent work analysed continental‐scale data on anthropogenic noise across the USA and found that passerine species inhabiting more noise‐polluted areas do not have higher peak song frequency but have more complex songs. However, this metric of song complexity is of ambiguous interpretation, because it can indicate either diverse syllables or a larger frequency bandwidth. In the latter case, the finding would support the noise filter hypothesis, because larger frequency bandwidths mean that more sound energy spreads to frequencies that are less masked by anthropogenic noise. We reanalysed how passerine song predicts exposure to noise using a more thorough dataset of acoustic song measurements, and showed that it is large frequency bandwidths, rather than diverse syllables, that predict the exposure of species to noise pollution. Given that larger bandwidths often encompass higher maximum frequencies, which are less masked by anthropogenic noise, our result suggests that tolerance to noise pollution might depend mostly on having the high‐frequency parts of song little masked by noise, thus preventing acoustic communication from going entirely unnoticed at long distances.