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1. Novel Insights to Be Gained From Applying Metacommunity Theory to Long-Term, Spatially Replicated Biodiversity Data

   https://doi.org/10.3389/fevo.2020.612794  

   Record, Sydne ; Voelker, Nicole M. ; Zarnetske, Phoebe L. ; Wisnoski, Nathan I. ; Tonkin, Jonathan D. ; Swan, Christopher ; Marazzi, Luca ; Lany, Nina ; Lamy, Thomas ; Compagnoni, Aldo ; et al ( January 2021 , Frontiers in Ecology and Evolution)

   null (Ed.)

   Global loss of biodiversity and its associated ecosystem services is occurring at an alarming rate and is predicted to accelerate in the future. Metacommunity theory provides a framework to investigate multi-scale processes that drive change in biodiversity across space and time. Short-term ecological studies across space have progressed our understanding of biodiversity through a metacommunity lens, however, such snapshots in time have been limited in their ability to explain which processes, at which scales, generate observed spatial patterns. Temporal dynamics of metacommunities have been understudied, and large gaps in theory and empirical data have hindered progress in our understanding of underlying metacommunity processes that give rise to biodiversity patterns. Fortunately, we are at an important point in the history of ecology, where long-term studies with cross-scale spatial replication provide a means to gain a deeper understanding of the multiscale processes driving biodiversity patterns in time and space to inform metacommunity theory. The maturation of coordinated research and observation networks, such as the United States Long Term Ecological Research (LTER) program, provides an opportunity to advance explanation and prediction of biodiversity change with observational and experimental data at spatial and temporal scales greater than any single research group could accomplish. Synthesis of LTER network community datasets illustrates that long-term studies with spatial replication present an under-utilized resource for advancing spatio-temporal metacommunity research. We identify challenges towards synthesizing these data and present recommendations for addressing these challenges. We conclude with insights about how future monitoring efforts by coordinated research and observation networks could further the development of metacommunity theory and its applications aimed at improving conservation efforts. 

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2. Synergies Among Environmental Science Research and Monitoring Networks: A Research Agenda

   https://doi.org/10.1029/2020EF001631  

   Jones, J. A. ; Groffman, P. M. ; Blair, J. ; Davis, F. W. ; Dugan, H. ; Euskirchen, E. E. ; Frey, S. D. ; Harms, T. K. ; Hinckley, E. ; Kosmala, M. ; et al ( March 2021 , Earth's Future)

   Many research and monitoring networks in recent decades have provided publicly available data documenting environmental and ecological change, but little is known about the status of efforts to synthesize this information across networks. We convened a working group to assess ongoing and potential cross‐network synthesis research and outline opportunities and challenges for the future, focusing on the US‐based research network (the US Long‐Term Ecological Research network, LTER) and monitoring network (the National Ecological Observatory Network, NEON). LTER‐NEON cross‐network research synergies arise from the potentials for LTER measurements, experiments, models, and observational studies to provide context and mechanisms for interpreting NEON data, and for NEON measurements to provide standardization and broad scale coverage that complement LTER studies. Initial cross‐network syntheses at co‐located sites in the LTER and NEON networks are addressing six broad topics: how long‐term vegetation change influences C fluxes; how detailed remotely sensed data reveal vegetation structure and function; aquatic‐terrestrial connections of nutrient cycling; ecosystem response to soil biogeochemistry and microbial processes; population and species responses to environmental change; and disturbance, stability and resilience. This initial study offers exciting potentials for expanded cross‐network syntheses involving multiple long‐term ecosystem processes at regional or continental scales. These potential syntheses could provide a pathway for the broader scientific community, beyond LTER and NEON, to engage in cross‐network science. These examples also apply to many other research and monitoring networks in the US and globally, and can guide scientists and research administrators in promoting broad‐scale research that supports resource management and environmental policy.

    

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3. Can dynamic network modelling be used to identify adaptive microbiomes?

   https://doi.org/10.1111/1365-2435.13491  

   Garcia, Joshua ; Kao‐Kniffin, Jenny ; Bennett, ed., Alison ( December 2019 , Functional Ecology)

   In recent times, interest has grown in understanding how microbiomes – the collection of microorganisms in a specific environment – influence the survivability or fitness of their plant and animal hosts. The profound diversity of bacterial and fungal species found in certain environments, such as soil, provides a large pool of potential microbial partners that can interact in ways that reveal patterns of associations linking host–microbiome traits developed over time. However, most microbiome sequence data are reported as a community fingerprint, without analysis of interaction networks across microbial taxa through time.

   To address this knowledge gap, more robust tools are needed to account for microbiome dynamics that could signal a beneficial change to a plant or animal host. In this paper, we discuss applying mathematical tools, such as dynamic network modelling, which involves the use of longitudinal data to study system dynamics and microbiomes that identify potential alterations in microbial communities over time in response to an environmental change. In addition, we discuss the potential challenges and pitfalls of these methodologies, such as handling large amounts of sequencing data and accounting for random processes that influence community dynamics, as well as potential ways to address them.

   Ultimately, we argue that components of microbial community interactions can be characterized through mathematical models to reveal insights into complex dynamics associated with a plant or animal host trait. The inclusion of interaction networks in microbiome studies could provide insights into the behaviour of complex communities in tandem with host trait modification and evolution.

   A freePlain Language Summarycan be found within the Supporting Information of this article.

    

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4. Resilience: insights from the U.S. LongTerm Ecological Research Network

   https://doi.org/10.1002/ecs2.3434  

   Cowles, Jane ; Templeton, Laura ; Battles, John J. ; Edmunds, Peter J. ; Carpenter, Robert C. ; Carpenter, Stephen R. ; Paul Nelson, Michael ; Cleavitt, Natalie L. ; Fahey, Timothy J. ; Groffman, Peter M. ; et al ( May 2021 , Ecosphere)

   Ecosystems are changing in complex and unpredictable ways, and analysis of these changes is facilitated by coordinated, long‐term research. Meeting diverse societal needs requires an understanding of what populations and communities will be dominant in 20, 50, and 100 yr. This paper is a product of a synthesis effort of the U.S. National Science Foundation funded Long‐Term Ecological Research (LTER) network addressing the LTER core research area of populations and communities. This analysis revealed that each LTER site had at least one compelling story about what their site would look like in 50 or 100 yr. As the stories were prepared, themes emerged, and the stories were grouped into papers along five themes for this special issue: state change, connectivity, resilience, time lags, and cascading effects. This paper addresses the resilience theme and includes stories from the Baltimore (urban), Hubbard Brook (northern hardwood forest), Andrews (temperate rain forest), Moorea (coral reef), Cedar Creek (grassland), and North Temperate Lakes (lakes) sites. The concept of resilience (the capacity of a system to maintain structure and processes in the face of disturbance) is an old topic that has seen a resurgence of interest as the nature and extent of global environmental change have intensified. The stories we present here show the power of long‐term manipulation experiments (Cedar Creek), the value of long‐term monitoring of forests in both natural (Andrews, Hubbard Brook) and urban settings (Baltimore), and insights that can be gained from modeling and/or experimental approaches paired with long‐term observations (North Temperate Lakes, Moorea). Three main conclusions emerge from the analysis: (1) Resilience research has matured over the past 40 yr of the LTER program; (2) there are many examples of high resilience among the ecosystems in the LTER network; (3) there are also many warning signs of declining resilience of the ecosystems we study. These stories highlight the need for long‐term studies to address this complex topic and show how the diversity of sites within the LTER network facilitates the emergence of overarching concepts about this important driver of ecosystem structure, function, services, and futures.

    

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5. Reviews and syntheses: The promise of big diverse soil data, moving current practices towards future potential

   https://doi.org/10.5194/bg-19-3505-2022  

   Todd-Brown, Katherine E. ; Abramoff, Rose Z. ; Beem-Miller, Jeffrey ; Blair, Hava K. ; Earl, Stevan ; Frederick, Kristen J. ; Fuka, Daniel R. ; Guevara Santamaria, Mario ; Harden, Jennifer W. ; Heckman, Katherine ; et al ( January 2022 , Biogeosciences)

   Abstract. In the age of big data, soil data are more available and richer than ever, but – outside of a few large soil survey resources – they remain largely unusable for informing soil management and understanding Earth system processes beyond the original study.Data science has promised a fully reusable research pipeline where data from past studies are used to contextualize new findings and reanalyzed for new insight.Yet synthesis projects encounter challenges at all steps of the data reuse pipeline, including unavailable data, labor-intensive transcription of datasets, incomplete metadata, and a lack of communication between collaborators.Here, using insights from a diversity of soil, data, and climate scientists, we summarize current practices in soil data synthesis across all stages of database creation: availability, input, harmonization, curation, and publication.We then suggest new soil-focused semantic tools to improve existing data pipelines, such as ontologies, vocabulary lists, and community practices.Our goal is to provide the soil data community with an overview of current practices in soil data and where we need to go to fully leverage big data to solve soil problems in the next century. 

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