Biology subjects

Arnold, W.

Publications and source records attributed to Arnold, W..

5 recordsLinked to original sources

bioRxiv2025

Tree microbiomes and methane emissions in upland forests

RationaleUpland forest trees emit CH , but whether emissions derive from internal microbial production or soil-derived transport remains debated. Methanogens have been detected in heartwood of several species, yet the prevalence of wood-associated methanogenesis, its metabolic basis, and its relationship to co-occurring methanotrophy are poorly understood. MethodsWe measured 1,148 stem fluxes and 276 soil fluxes, sampled internal stem gases including {delta}{superscript 1}3CH , quantified methanogens and methanotrophs via ddPCR in 564 samples, characterized communities via 16S rRNA sequencing, and upscaled fluxes. Key resultsMethanogens were detected in 97% of heartwood samples (up to 10 copies g {superscript 1}) at concentrations exceeding soil by [~]2 orders of magnitude; methane consumers were likewise near-ubiquitous across forest compartments. Wood harbored distinct microbial communities dominated by hydrogenotrophic Methanobacteriaceae, corroborated by depleted {delta}{superscript 1}3CH . Vertical flux profiles indicated soil transport only in wet microsites, with uniform emissions across height consistent with internal production across most upland species. Species-level methanogen:methanotroph ratios predicted emissions (R{superscript 2} = 0.51), indicating net flux reflects the balance between production and oxidation. Main conclusionMethane-cycling microbes are widespread in upland trees, and net methane flux reflects the species-level balance between production and consumption. Internal methanogenesis contributes widely to upland tree emissions; resolving ecosystem-scale magnitude requires improved quantification of woody surface area and vertical flux variability.

ecology↗

bioRxiv2024

A diverse and distinct microbiome inside living trees

Despite significant advances in microbiome research across various environments1, the microbiome of Earths largest biomass reservoir- the wood of living trees2- remains largely unexplored. This oversight neglects a critical aspect of global biodiversity and potentially key players in tree health and forest ecosystem functions. Here we illuminate the microbiome inhabiting and adapted to wood, and further specialized to individual host species. We demonstrate that a single tree can host approximately a trillion microbes in its aboveground internal tissues, with microbial communities partitioned between heartwood and sapwood, each maintaining a distinct microbiome with minimal similarity to other plant tissues or nearby ecosystem components. Notably, the heartwood microbiome emerges as a unique ecological niche, distinguished in part by endemic archaea and anaerobic bacteria that drive consequential biogeochemical processes. Our research supports the emerging idea of a plant as a "holobiont"3,4--a single ecological unit comprising host and associated microorganisms--and parallels human microbiome research in its implications for host health, disease, and functionality5. By mapping the structure, composition, and potential sources and functions of the tree internal microbiome, our findings pave the way for novel insights into tree physiology and forest ecology, and establish a new frontier in environmental microbiology.

ecology↗

bioRxiv2023

A Method for Sampling the Living Wood Microbiome

Efforts to characterize microbial life across diverse environments have progressed tremendously, yet the microbiome of Earths largest biomass reservoir--the wood of living trees--has been largely unexplored. Current understanding of the tree microbiome is largely confined to roots and leaves, with little attention given to the endophytic microbiome of wood, even though emergent studies have indicated this zone as a niche for unique taxa, of consequence for ecosystem health and global biogeochemical cycles. The lack of investigation derives partly from the physical recalcitrance of wood, which presents challenges during sampling, homogenization, and the extraction of nucleic acids. In response to these issues, we present an optimized method for processing wood for use in microbial analyses, from sampling through to downstream analyses. Using methane-cycling taxa as model endophytes, we assess losses in recovery during our method, and determine a limit-of-detection of approximately 500 cells per 100 mg of (dry) wood. For all six species evaluated--which represented several diverse taxa of hardwoods and softwoods--PCR inhibition proved minimal, and we expect this method to be applicable for a majority of tree species. The methods presented herein can facilitate future investigation into the wood microbiome and global microbial ecology of methane cycling.

ecology↗

bioRxiv2018

Muscle nonshivering thermogenesis in a feral mammal

While small mammals and neonates are able to maintain an optimal body temperature (Tb) independent of ambient conditions by producing heat via nonshivering thermogenesis (NST) in the brown adipose tissue (BAT), larger mammals and other mammals lacking BAT were long believed to rely primarily on shivering and behavioural adaptations. However, recently, a second mechanism of NST was found in skeletal muscle that could play an important role in thermoregulation of such species. Muscle NST is independent of muscle contractions and produces heat based on the activity of an ATPase pump in the sarcoplasmic reticulum (SERCA1a) and controlled by the protein sarcolipin. To evaluate whether muscle NST could indeed play an important role in thermoregulation in species lacking BAT, we investigated the thermogenic capacities of new-born wild boar piglets. During cold exposure over the first 5 days of life, total heat production was improved while shivering intensity decreased, indicating an increasing contribution of NST. Sampling skeletal muscle tissue for analyses of SERCA activity as well as gene expression of SERCA1a and sarcolipin, we found an age-related increase in all three variables as well as in Tb. Hence, the improved thermogenesis during the development of wild boars is not due to shivering but explained by the observed increase in SERCA activity. Our results suggest that muscle NST may be the primary mechanism of heat production during cold stress in large mammals lacking BAT, strengthening the hypothesis that muscle NST has likely played an important role in the evolution of endothermy.

physiology↗

bioRxiv2018

DNA Methylation by Restriction Modification Systems Affects the Global Transcriptome Profile in Borrelia burgdorferi

Prokaryote restriction modification (RM) systems serve to protect bacteria from potentially detrimental foreign DNA. Recent evidence suggests that DNA methylation by the methyltransferase (MTase) components of RM systems can also have effects on transcriptome profiles. The causative agent of Lyme disease, Borrelia burgdorferi, encodes two RM systems with N6-Methyladenosine (m6A) MTase activity. The specific recognition and/or methylation sequences have not been identified for either B. burgdorferi MTase, and it is not currently known whether these RM systems influence transcriptome profiles. In the current study, Single Molecule Real Time sequencing was utilized to map genome-wide m6A sites, and to identify consensus modified motifs in wild-type B. burgdorferi as well as isogenic MTase mutants. Four conserved m6A motifs were identified, and were fully attributable to the presence of specific MTases. Whole-genome transcriptome changes were observed in conjunction with the loss of MTase enzymes, indicating that DNA methylation by RM systems has effects on gene expression in B. burgdorferi. The results of this study provide a comprehensive view of the DNA methylation pattern in B. burgdorferi, and the accompanying gene expression profiles add to the emerging body of research on RM systems and gene regulation in bacteria.\n\nIMPORTANCELyme disease is the most prevalent vector-borne disease in North America, and is classified by the Centers for Disease Control and Prevention (CDC) as an emerging infectious disease with an expanding geographical area of occurrence. Previous studies have shown that the causative bacterium, Borrelia burgdorferi, methylates its genome using restriction modification systems that allow for the distinction of self from foreign DNA. Although much research has focused on the regulation of gene expression in B. burgdorferi, the effects of DNA methylation on gene regulation has not been evaluated. The current study characterizes the patterns of DNA methylation by restriction modification systems in B. burgdorferi, and evaluates the resulting effects on gene regulation in this important pathogen.

microbiology↗