Biology subjects

Honeyman, A. S.

Publications and source records attributed to Honeyman, A. S..

4 recordsLinked to original sources

bioRxiv2022

Statistical learning and uncommon soil microbiota explain biogeochemical responses after wildfire

1Wildfires are a perennial event globally and the biogeochemical underpinnings of soil responses at relevant spatial and temporal scales are unclear. Soil biogeochemical processes regulate plant growth and nutrient losses that affect water quality, yet the response of soil after variable intensity fire is difficult to explain and predict. To address this issue, we examined two wildfires in Colorado, USA across the first and second post-fire years and leveraged Statistical Learning (SL) to predict and explain biogeochemical responses. We found that SL predicts biogeochemical responses in soil after wildfire with surprising accuracy. Of the 13 biogeochemical analytes analyzed in this study, 9 are best explained with a hybrid microbiome + biogeochemical SL model. Biogeochemical-only models best explain 3 features, and 1 feature is explained equally well with hybrid or biogeochemical-only models. In some cases, microbiome-only SL models are also effective (such as predicting NH4+). Whenever a microbiome component is employed, selected features always involve uncommon soil microbiota (i.e., the rare biosphere, existing at < 1% relative abundance). Here, we demonstrate that SL paired with DNA sequence and biogeochemical data predict environmental features in post-fire soils, though this approach could likely be applied to any biogeochemical system.

microbiology↗

bioRxiv2021

Spatial and temporal constraints on the composition of microbial communities in subsurface boreholes of the Edgar Experimental Mine

The deep biosphere hosts uniquely adapted microorganisms overcoming geochemical extremes at significant depths within the crust of the Earth. While numerous novel microbial members with unique physiological modifications remain to be identified, even greater attention is required to understand the near-subsurface and its continuity with surface systems. This raises key questions about networking of surface hydrology, geochemistry affecting near-subsurface microbial composition, and resiliency of subsurface ecosystems. Here, we apply molecular and geochemical approaches to determine temporal microbial composition and environmental conditions of filtered borehole fluid from the Edgar Experimental Mine ([~]150 meters below the surface) in Idaho Springs, CO. Samples were collected over a 4-year collection period from expandable packers deployed to accumulate fluid in previously drilled boreholes located centimeters to meters apart, revealing temporal evolution of borehole microbiology. Meteoric water feeding boreholes demonstrated variable recharge rates likely due to a complex and undefined fracture system within the host rock. 16S rRNA gene analysis determined unique microbial communities occupy the four boreholes examined. Two boreholes yielded sequences revealing the presence of Proteobacteria, Firmicutes, and Nanoarcheota associated with endemic subsurface communities. Two other boreholes presented sequences related to soil-originating microbiota, which likely indicate a direct link to surface infiltration. High concentrations of sulfate suggest sulfur-related metabolic strategies dominate within these near-subsurface boreholes. Overall, results indicate microbial community composition in the near-subsurface is highly dynamic at very fine spatial scales (<20cm) within fluid-rock equilibrated boreholes, which additionally supports the role of a relationship for surface geochemical processes infiltrating and influencing subsurface environments. ImportanceThe Edgar Experimental Mine, Idaho Springs, Colorado provides inexpensive and open access to borehole investigations for subsurface microbiology studies. Understanding how microbial processes in the near-subsurface are connected to surface hydrological influences like meteoric input is lacking. Investigating microbial communities of subsurface mine boreholes provides evidence of how geochemical processes are linked to biogeochemical processes within each borehole, and the geochemical connectedness and mobility of surface influences. This study details microbial community composition and fluid geochemistry over spatial and temporal scales from boreholes within the Edgar Mine. These findings are relevant to biogeochemistry of near-surface mines, caves and other voids across planetary terrestrial systems. In addition, this work can lead to understanding how microbial communities relating to both fluid-rock equilibration and geochemical influences may enhance our understanding of subsurface molecular biological tools that aid mining economic practices to reflect biological signals for lucrative veins in the near subsurface.

microbiology↗

bioRxiv2020

Microbially-mediated pretreatment of aerated oil and gas produced water by addition of phosphorous or activated sludge

Produced Water (PW) from oil and gas (O&G) producing wells is a unique source of water in water-stressed regions. Microbiota within O&G formations have been well-studied on site/in-situ, but few applied works have considered their role in the treatment of PW in engineered water treatment systems. Herein, we operated a simple aeration/mixing bench-scale bioreactor fed with produced water under three conditions: 1) PW alone (control; hereafter referred to as baseline), 2) phosphorous dosed daily as KH2PO4, and 3) activated sludge (AS) dosed daily from a sequence batch membrane bioreactor (SB-MBR). Aerated and mixed PW alone (baseline) was able to attenuate PW chemistry with removal of soluble chemical oxygen demand (sCOD) and ammonia by 27.6% and 17.8%, respectively. Further KH2PO4 and AS additions improved water treatment efficiency markedly; in the KH2PO4 addition reactor, sCOD and ammonia were reduced by 50.0% and 61.5%, respectively, and in the AS addition reactor by 52.5% and 59.2%, respectively. Microbial consortia determined via 16S rRNA gene amplicons differ in composition between raw PW and all reactors; order Kiloniellales was most common in raw PW while orders Rhodobacterales, Pseudomonadales, and Caulobacterales were most abundant amongst AS, KH2PO4, and baseline conditions, respectively. Several different microbial consortia are capable of treating raw PW which suggests that functional redundancy amongst microbiota in engineered treatment systems may be underappreciated. With simple addition of phosphorous and/or activated sludge to PW as part of a treatment strategy, a higher quality water can then be subjected to conventional treatment and/or local reuse. ImportanceMultiple microbiological communities are capable of treating O&G PW in a simple, applied, engineered setting. The broad possibility of PW treatment by multiple different microbial consortia elucidates the potential for easy, effective, water reuse processes in the hydraulically-stressed arid west as well as any region generating PW from O&G operations.

microbiology↗

bioRxiv2018

Fresh Snowfall Microbiology and Chemistry are Driven by Geography in Storm-Tracked Events

Snowfall is a global phenomenon highly integrated with hydrology and ecology. Forays into studying bioaerosols and their dependence on aeolian movement are largely constrained to either precipitation-independent analyses or in-silico models. Though snowpack and glacial microbiological studies have been conducted, little is known about the biological component of meteoric snow. Through culture-independent phylogenetic and geochemical analyses, we show that the geographical location at which snow precipitates determines snowfalls geochemical and microbiological composition. Storm-tracking, furthermore, can be used as a valuable environmental indicator to trace down what factors are influencing bioaerosols. We estimate annual deposits of up to ~10 kg of bacterial / archaeal biomass per hectare along our study area of the eastern Front Range in Colorado. The dominant kinds of microbiota captured in an analysis of seven snow events at two different locations, one urban, one rural, across the winter of 2016/2017 included phyla Proteobacteria, Bacteroidetes, Firmicutes and Acidobacteria, though a multitude of different kinds of organisms were found in both. Taxonomically, Bacteroidetes were more abundant in Golden (urban plain) snow while Proteobacteria were more common in Sunshine (rural mountain) samples. Chemically, Golden snowfall was positively correlated with some metals and anions. The work also hints at better informing the everything is everywhere hypotheses of the microbial world and that atmospheric transport of microbiota is not only common, but is capable of disseminating vast amounts of microbiota of different physiologies and genetics that then affect ecosystems globally. Snowfall, we conclude, is a significant repository of microbiological material with strong implications for both ecosystem genetic flux and general bio-aerosol theory.\n\nImportanceSnowfall is commonplace to the temperate and polar regions of the world. As an interface between the atmosphere, hydrosphere and earth, snow is responsible for high annual deposits of moisture globally, and, can serve as a water bank in the form of both permanent snow fields and glaciers. Essential to general ecosystem function, snow can also be considered a transporter of aerosolized material. Given the magnitude of microbiota deposited by snowfall, which we report, it is likely that biological material within snowfall, with its geochemical underpinning-- and the associated genetic banks--have significant downstream ecological effects.\n\nUnderstanding what is contained in snowfall becomes especially urgent in a warming climate where high-impact meteorological and ecological changes are imminent and likely. With climate-induced changes to snowfall patterns, surface ecosystems are likely to be impacted by ensuing changes in microbiota deposition. Thus, the ecosystem function of soils, rock and surface waters are also likely to be impacted; these changes, in turn, greatly influence agriculture, weathering and infrastructure.

microbiology↗