Limited genomic signatures of population collapse in the critically endangered black abalone (Haliotis cracherodii)

The black abalone, Haliotis cracherodii, is a large, long-lived marine mollusc that inhabits rocky intertidal habitats along the coast of California and Mexico. In 1985, populations were impacted by a bacterial disease known as withering syndrome (WS) that wiped out >90% of individuals, leading to the closure of all U.S. black abalone fisheries since 1993. Current conservation strategies include restoring diminished populations by translocating healthy individuals. However, population collapse on this scale may have dramatically lowered genetic diversity and strengthened geographic differentiation, making translocation-based recovery contentious. Additionally, the current prevalence of WS remains unknown. To address these uncertainties, we sequenced and analysed the genomes of 133 black abalone individuals from across their present range. We observed no spatial genetic structure among black abalone, with the exception of a single chromosomal inversion that increases in frequency with latitude. Outside the inversion, genetic differentiation between sites is minimal and does not scale with either geographic distance or environmental dissimilarity. Genetic diversity appears uniformly high across the range. Demographic inference does indicate a severe population bottleneck beginning just 15 generations in the past, but this decline is short lived, with present-day size far exceeding the pre-bottleneck status quo. Finally, we find the bacterial agent of WS is equally present across the sampled range, but only in 10% of individuals. The lack of population genetic structure, uniform diversity and prevalence of WS bacteria indicates that translocation could be a valid and low-risk means of population restoration for black abalone species' recovery.

Limited genomic signatures of population collapse in the critically endangered black abalone (Haliotis cracherodii)

The black abalone, Haliotis cracherodii, is a large, long-lived marine mollusc that inhabits rocky intertidal habitats along the coast of California and Mexico. In 1985, populations were impacted by a bacterial disease known as withering syndrome (WS) that wiped out >90% of individuals, leading to the species' designation as critically endangered. Current conservation strategies include restoring diminished populations by translocating healthy individuals. However, population collapse on this scale may have dramatically lowered genetic diversity and strengthened geographic differentiation, making translocation-based recovery contentious. Additionally, the current prevalence of WS is unknown. To address these uncertainties, we sequenced and analyzed the genomes of 133 black abalone individuals from across their present range. We observed no spatial genetic structure among black abalone, with the exception of a single chromosomal inversion that increases in frequency with latitude. Genetic divergence between sites is minimal, and does not scale with either geographic distance or environmental dissimilarity. Genetic diversity appears uniformly high across the range. Despite this, however, demographic inference confirms a severe population bottleneck beginning around the time of WS onset, highlighting the temporal offset that may occur between a population collapse and its potential impact on genetic diversity. Finally, we find the bacterial agent of WS is equally present across the sampled range, but only in 10% of individuals. The lack of genetic structure, uniform diversity, and prevalence of WS bacteria indicates that translocation could be a valid and low-risk means of population restoration for black abalone species' recovery.

A Draft Reference Genome Assembly of the Critically Endangered Black Abalone, Haliotis cracherodii

The once abundant black abalone, Haliotis cracherodii, is a large, long-lived grazing marine mollusk that inhabits the rocky intertidal along the coast of California. The species has experienced dramatic declines since the mid-1980s largely due to the fatal bacterial disease called withering syndrome, leading to the collapse of an economically important fishery and to its inclusion into the IUCN listing as a critically endangered species. In some places impacted by the disease, populations of black abalone have declined by more than 90%, prompting population crashes associated with very little recruitment of new individuals and changes to intertidal communities. Habitats that were dominated by crustose coralline algae and bare rock have become dominated instead by fleshy algae and sessile invertebrates. Here, we present the first high-quality black abalone reference genome, assembled with PacBio HiFi long-reads and assembled with Dovetail Omni-C data to generate a scaffold-level assembly. The black abalone reference genome will be an essential resource in understanding the evolutionary history of this species as well as for exploring its current levels of genetic diversity and establishing future management and restoration plans.

Ten strategies for a successful transition to remote learning: Lessons learned with a flipped course

Transitioning from in-person to remote learning can present challenges for both the instructional team and the students. Here, we use our course "Biodiversity in the Age of Humans" to describe how we adapted tools and strategies designed for a flipped classroom to a remote learning format. Using anonymous survey data collected from students who attended the course either in-person (2019) or remotely (2020), we quantify student expectations and experiences and compare these between years. We summarize our experience and provide ten "tips" or recommendations for a transition to remote learning, which we divide into three categories: (a) precourse instructor preparation; (b) outside of class use of online materials; and (c) during class student engagement. The survey results indicated no negative impact on student learning during the remote course compared to in-person instruction. We found that communicating with students and assessing specific needs, such as access to technology, and being flexible with the structure of the course, simplified the transition to remote instruction. We also found that short, pre-recorded videos that introduce subject materials were among the most valuable elements for student learning. We hope that instructors of undergraduate ecology and evolution courses can use these recommendations to help establish inclusive online learning communities that empower students to acquire conceptual knowledge and develop scientific inquiry and literacy skills.

Lake characteristics influence how methanogens in littoral sediments respond to terrestrial litter inputs

Shallow lake sediments harbor methanogen communities that are responsible for large amounts of CH₄ flux to the atmosphere. These communities play a major role in degrading in-fluxed terrestrial organic matter (t-OM)-much of which settles in shallow near-shore sediments. Little work has examined how sediment methanogens are affected by the quantity and quality of t-OM, and the physicochemical factors that shape their community. Here, we filled mesocosms with artificial lake sediments amended with different ratios and concentrations of coniferous and deciduous tree litter. We installed them in three boreal lakes near Sudbury, Canada that varied in trophic status and water clarity. We found that higher endogenous nutrient concentrations led to greater CH₄ production when sediment solar irradiance was similar, but high irradiance of sediments also led to higher CH₄ concentrations regardless of nutrient concentrations, possibly due to photooxidation of t-OM. Sediments with t-OM had overall higher CH₄ concentrations than controls that had no t-OM, but there were no significant differences in CH₄ concentrations with different t-OM compositions or increasing concentrations over 25%. Differences among lakes also explained variation in methanogen community structure, whereas t-OM treatments did not. Therefore, lake characteristics are important modulators of methanogen communities fueled by t-OM.

Ten-year assessment of the 100 priority questions for global biodiversity conservation

In 2008, a group of conservation scientists compiled a list of 100 priority questions for the conservation of the world's biodiversity. However, now almost a decade later, no one has yet published a study gauging how much progress has been made in addressing these 100 high-priority questions in the peer-reviewed literature. We took a first step toward reexamining the 100 questions to identify key knowledge gaps that remain. Through a combination of a questionnaire and a literature review, we evaluated each question on the basis of 2 criteria: relevance and effort. We defined highly relevant questions as those that - if answered - would have the greatest impact on global biodiversity conservation and quantified effort based on the number of review publications addressing a particular question, which we used as a proxy for research effort. Using this approach, we identified a set of questions that, despite being perceived as highly relevant, have been the focus of relatively few review publications over the past 10 years. These questions covered a broad range of topics but predominantly tackled 3 major themes: conservation and management of freshwater ecosystems, role of societal structures in shaping interactions between people and the environment, and impacts of conservation interventions. We believe these questions represent important knowledge gaps that have received insufficient attention and may need to be prioritized in future research.

Microbiome functioning depends on individual and interactive effects of the environment and community structure

How ecosystem functioning changes with microbial communities remains an open question in natural ecosystems. Both present-day environmental conditions and historical events, such as past differences in dispersal, can have a greater influence over ecosystem function than the diversity or abundance of both taxa and genes. Here, we estimated how individual and interactive effects of microbial community structure defined by diversity and abundance, present-day environmental conditions, and an indicator of historical legacies influenced ecosystem functioning in lake sediments. We studied sediments because they have strong gradients in all three of these ecosystem properties and deliver important functions worldwide. By characterizing bacterial community composition and functional traits at eight sites fed by discrete and contrasting catchments, we found that taxonomic diversity and the normalized abundance of oxidase-encoding genes explained as much variation in CO₂ production as present-day gradients of pH and organic matter quantity and quality. Functional gene diversity was not linked to CO₂ production rates. Surprisingly, the effects of taxonomic diversity and normalized oxidase abundance in the model predicting CO₂ production were attributable to site-level differences in bacterial communities unrelated to the present-day environment, suggesting that colonization history rather than habitat-based filtering indirectly influenced ecosystem functioning. Our findings add to limited evidence that biodiversity and gene abundance explain patterns of microbiome functioning in nature. Yet we highlight among the first time how these relationships depend directly on present-day environmental conditions and indirectly on historical legacies, and so need to be contextualized with these other ecosystem properties.

Fifty important research questions in microbial ecology

Microbial ecology provides insights into the ecological and evolutionary dynamics of microbial communities underpinning every ecosystem on Earth. Microbial communities can now be investigated in unprecedented detail, although there is still a wealth of open questions to be tackled. Here we identify 50 research questions of fundamental importance to the science or application of microbial ecology, with the intention of summarising the field and bringing focus to new research avenues. Questions are categorised into seven themes: host-microbiome interactions; health and infectious diseases; human health and food security; microbial ecology in a changing world; environmental processes; functional diversity; and evolutionary processes. Many questions recognise that microbes provide an extraordinary array of functional diversity that can be harnessed to solve real-world problems. Our limited knowledge of spatial and temporal variation in microbial diversity and function is also reflected, as is the need to integrate micro- and macro-ecological concepts, and knowledge derived from studies with humans and other diverse organisms. Although not exhaustive, the questions presented are intended to stimulate discussion and provide focus for researchers, funders and policy makers, informing the future research agenda in microbial ecology.