Search

This special feature presents state-of-the-art soil ecological science and was sparked following the 2-day long online live event entitled “Ecology Underground” during the Ecological Society of America annual meeting of 2020. Here, we, the co-guest-editors of this special feature, present this body of research in context of the current state of the field. This issue highlights that we are currently in a hot time for microbial research in soil science. Specifically, we find that two themes emerge from this corpus as key next questions to answer to move the field forward. How do microbial processes scale up in space and time? And how do they respond to multiple interacting global change factors?

Rising to meet global, interconnected challenges, such as food security and ecosystem resilience to global change, requires insights from across the Earth. This is especially true for belowground terrestrial ecological processes. Soil ecologists have answered this call: like mushrooms, large global datasets and databases on soil physics, chemistry and ecology are sprouting up everywhere (e.g. Fine‐Root Ecology Database (Iversen et al., 2018), FunFun (Zanne et al., 2020), GlobalFungi (Větrovský et al., 2020), COntinuous SOil REspiration (Jian et al., 2020), Global distribution of earthworm diversity (Philips et al., 2019) etc.). It is now time to leverage synergies among these datasets to link the continuum of belowground processes to ecosystem functions (e.g. decomposition, nutrient cycling and soil respiration). Built on interdisciplinary and international collaborations, data synthesis that leads to a holistic understanding is one of the best ways of predicting the future of terrestrial ecosystems and for preserving ecosystem services under global change. In 2020, global interconnectedness was on display as we saw a pandemic sweep across the world in weeks. The pandemic allowed the Ecological Society of America (ESA) to enter a new digital era by holding a fully virtual conference. While technology cannot yet replicate all aspects of an in‐person conference, the virtual platform increased accessibility and reduced the climate impact of the annual conference. It also provided an opportunity for early‐career plant and microbial ecologists from five ESA Organized Oral Sessions and one Inspire Session to organize Ecology Underground, a two‐day program of live virtual talks and open discussions on integrative belowground ecology on 4 and 5 August 2020. Ecology Underground was sponsored by New Phytologist, the ESA Soil Ecology Section, the US Department of Energy, Biological and Environmental Research program and the Oak Ridge Institute for Science and Education (ORISE), and gathered 453 participants over two days. The online platform allowed for participation across the globe (37 countries were represented; Fig. 1) and was an opportunity to think creatively about how scientific discussions and global collaborations can take place, now and in the future. Open in a separate window Fig. 1 The online platform of Ecology Underground allowed for participation across the globe.

Peatlands are a climate critical carbon (C) reservoir that will likely become a C source under continued warming. A strong relationship between plant tissue chemistry and the soil organic matter (SOM) that fuels C gas emissions is inferred, but rarely examined at the molecular level. Here we compared Fourier transform infrared (FT-IR) spectroscopy measurements of solid phase functionalities in plants and SOM to ultra-high-resolution mass spectrometric analyses of plant and SOM water extracts across a palsa-bog-fen thaw and moisture gradient in an Arctic peatland. From these analyses we calculated the C oxidation state (NOSC), a measure which can be used to assess organic matter quality. Palsa plant extracts had the highest NOSC, indicating high quality, while extracts ofSphagnum, which dominated the bog, had the lowest NOSC. The percentage of plant compounds that are less bioavailable and accumulate in the peat, increases from palsa (25%) to fen (41%) to bog (47 %), reflecting the pattern of percentSphagnumcover. The pattern of NOSC in the plant extracts was consistent with the high number of consumed compounds in the palsa and low number of consumed compounds in the bog. However, in the FT-IR analysis of the solid phase bog peat, carbohydrate content was high implying higher quality SOM. We explain this discrepancy as the result of low solubilization of bog SOM facilitated by the low pH in the bog which makes the solid phase carbohydrates less available to microbial decomposition. Plant-associated lignins and tannins declined in the unsaturated palsa peat indicating decomposition, but accumulated in the bog and fen peat where decomposition was presumably inhibited by the anaerobic conditions. A molecular-level comparison of the aboveground C sources and peat SOM demonstrates that climate-associated vegetation shifts in peatlands are important controls on the mechanisms underlying changing C gas emissions.

Peatlands represent large terrestrial carbon banks. Given that most peat accumulates in boreal regions, where low temperatures and water saturation preserve organic matter, the existence of peat in (sub)tropical regions remains enigmatic. Here we examined peat and plant chemistry across a latitudinal transect from the Arctic to the tropics. Near-surface low-latitude peat has lower carbohydrate and greater aromatic content than near-surface high-latitude peat, creating a reduced oxidation state and resulting recalcitrance. This recalcitrance allows peat to persist in the (sub)tropics despite warm temperatures. Because we observed similar declines in carbohydrate content with depth in high-latitude peat, our data explain recent field-scale deep peat warming experiments in which catotelm (deeper) peat remained stable despite temperature increases up to 9 °C. We suggest that high-latitude deep peat reservoirs may be stabilized in the face of climate change by their ultimately lower carbohydrate and higher aromatic composition, similar to tropical peats., Large peatlands exist at high latitudes because flooded conditions and cold temperatures slow decomposition, so the presence of (sub)tropical peat is enigmatic. Here the authors show that low-latitude peat is preserved due to lower carbohydrate and greater aromatic content resulting in chemical recalcitrance.

A major challenge in predicting the response of both social-hydrological and social-ecological systems to environmental change is the lack of a causal framework for predicting thresholds of change between the linked social and natural components. Here we propose a social-ecohydrological thresholds (SEHT) framework that integrates social-hydrological, trait-based ecological, and ecosystem services concepts. This approach facilitates the identification of thresholds by treating ecosystem services as indicators of the coupling of social and natural components of the system. Using the San Pedro riparian corridor in Arizona as a case study, we implemented the SEHT framework using ecological research and stakeholder perspectives to identify key drivers and thresholds in the social-ecohydrological system. In this way, we were able to describe expected outcomes of different hydrological change scenarios on the system. Stakeholders provided input on the utility of this information to inform management decisions aimed at mitigating the impacts of environmental change. The SEHT framework provides insight on dynamics of ecosystem services. This paper demonstrates that application of the framework enables the identification of several critical drivers of potential thresholds in ecosystem services that derive from either natural or social components of the overall system. These potential thresholds can guide ecosystem service assessment and monitoring and provide a roadmap for environmental management and the development of management scenarios.

Plant-associated microbiomes are structured by environmental conditions and plant associates, both of which are being altered by climate change. The future structure of plant microbiomes will depend on the, largely unknown, relative importance of each. This uncertainty is particularly relevant for arctic peatlands, which are undergoing large shifts in plant communities and soil microbiomes as permafrost thaws, and are potentially appreciable sources of climate change feedbacks due to their soil carbon (C) storage. We characterized phyllosphere and rhizosphere microbiomes of six plant species, and bulk peat, across a permafrost thaw progression (from intact permafrost, to partially- and fully-thawed stages) via 16S rRNA gene amplicon sequencing. We tested the hypothesis that the relative influence of biotic versus environmental filtering (the role of plant species versus thaw-defined habitat) in structuring microbial communities would differ among phyllosphere, rhizosphere, and bulk peat. Using both abundance- and phylogenetic-based approaches, we found that phyllosphere microbial composition was more strongly explained by plant associate, with little influence of habitat, whereas in the rhizosphere, plant and habitat had similar influence. Network-based community analyses showed that keystone taxa exhibited similar patterns with stronger responses to drivers. However, plant associates appeared to have a larger influence on organisms belonging to families associated with methane-cycling than the bulk community. Putative methanogens were more strongly influenced by plant than habitat in the rhizosphere, and in the phyllosphere putative methanotrophs were more strongly influenced by plant than was the community at large. We conclude that biotic effects can be stronger than environmental filtering, but their relative importance varies among microbial groups. For most microbes in this system, biotic filtering was stronger aboveground than belowground. However, for putative methane-cyclers, plant associations have a stronger influence on community composition than environment despite major hydrological changes with thaw. This suggests that plant successional dynamics may be as important as hydrological changes in determining microbial relevance to C-cycling climate feedbacks. By partitioning the degree that plant versus environmental filtering drives microbiome composition and function we can improve our ability to predict the consequences of warming for C-cycling in other arctic areas undergoing similar permafrost thaw transitions.

Modern microbial and ecosystem sciences require diverse interdisciplinary teams that are often challenged in “speaking” to one another due to different languages and data product types. Here we introduce the IsoGenie Database (IsoGenieDB; https://isogenie-db.asc.ohio-state.edu/), a de novo developed data management and exploration platform, as a solution to this challenge of accurately representing and integrating heterogenous environmental and microbial data across ecosystem scales. The IsoGenieDB is a public and private data infrastructure designed to store and query data generated by the IsoGenie Project, a ~10 year DOE-funded project focused on discovering ecosystem climate feedbacks in a thawing permafrost landscape. The IsoGenieDB provides (i) a platform for IsoGenie Project members to explore the project’s interdisciplinary datasets across scales through the inherent relationships among data entities, (ii) a framework to consolidate and harmonize the datasets needed by the team’s modelers, and (iii) a public venue that leverages the same spatially explicit, disciplinarily integrated data structure to share published datasets. The IsoGenieDB is also being expanded to cover the NASA-funded Archaea to Atmosphere (A2A) project, which scales the findings of IsoGenie to a broader suite of Arctic peatlands, via the umbrella A2A Database (A2A-DB). The IsoGenieDB’s expandability and flexible architecture allow it to serve as an example ecosystems database.