Biology subjects

Richter, D. D.

Publications and source records attributed to Richter, D. D..

2 recordsLinked to original sources

bioRxiv2023

The Primacy of Temporal Dynamics in Driving Spatial Self-organization of Soil Redox Patterns

In this study, we investigate mechanisms that generate regularly-spaced, iron banding in upland soils. These redoximorphic features appear in soils worldwide, but their genesis has been heretofore unresolved. Upland soils are highly redox dynamic, with significant redox fluctuations driven by rainfall, groundwater changes, or irrigation. Pattern formation in these highly dynamic systems provides an opportunity to investigate the temporal dimension of spatial self-organization, which is not often explored. By comparing multiple alternative mechanisms, we find that regular redox patterns in upland soils are formed by coupling two sets of scale-dependent feedbacks (SDF), the general framework underlying Turing instability. The first set of SDF is based on clay aggregation and disaggregation. The second set is realized by threshold-dependent, negative root responses to aggregated crystalline Fe(III). The former SDF amplifies Fe(III) aggregation and crystallinity to trigger the latter SDF. Neither set of SDF alone is sufficient to reproduce observed patterns. Redox oscillations driven by environmental variability play an indispensable role in pattern formation. Environmental variability creates a range of conditions at the same site for various processes in SDF to occur, albeit in different temporal windows of differing durations. In effect, environmental variability determines mean rates of pattern-forming processes over the timescale relevant to pattern formation and modifies the likelihood that pattern formation will occur. As such, projected climate change might significantly alter many self-organized systems, as well as the ecological consequences associated with the striking patterns they present. This temporal dimension of pattern formation is previously unreported and merits close attention. Statement of SignificanceIron reactions create redox features in soils around the world. This study investigates mechanisms forming regularly-spaced iron stripes in upland soils. Upland soil redox conditions, driven by environmental variability, are highly dynamic. We show that two sets of scale-dependent feedbacks are coupled to form redox patterns and environmental variability plays a critical role in both. Significantly, environmental variability creates opportunities for various pattern-forming processes to occur at the same site in different temporal windows and determines mean process rates over the timescale relevant to pattern formation. Hence, environmental variability dictates the likelihood of pattern formation. Such a critical role of the temporal dimension in spatial self-organization has rarely been reported and has great potential for application in other self-organized ecosystems.

ecology↗

bioRxiv2019

Ecological and genomic attributes of novel bacterial taxa that thrive in subsurface soil horizons

While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the U.S. to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.\n\nImportanceSoil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the U.S., we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored distinct communities compared to the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising amount of novel microbes with unique adaptations to oligotrophic subsurface conditions.

microbiology↗