Biology subjects

Raymond, P. A.

Publications and source records attributed to Raymond, P. A..

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↗

bioRxiv2019

Defect patterns on the curved surface of fish retinae suggest mechanism of cone mosaic formation

The outer epithelial layer of zebrafish retinae contains a crystalline array of cone photoreceptors, called the cone mosaic. As this mosaic grows by mitotic addition of new photoreceptors at the rim of the hemispheric retina, topological defects, called \"Y-Junctions\", form to maintain approximately constant cell spacing. The generation of topological defects due to growth on a curved surface is a distinct feature of the cone mosaic not seen in other well-studied biological patterns like the R8 photoreceptor array in the Drosophila compound eye. Since defects can provide insight into cell-cell interactions responsible for pattern formation, we characterize the arrangement of cones in individual Y-Junction cores as well as the spatial distribution of Y-junctions across entire retinae. We find that for individual Y-junctions, the distribution of cones near the core corresponds closely to structures observed in physical crystals. In addition, Y-Junctions are organized into lines, called grain boundaries, from the retinal center to the periphery. In physical crystals, regardless of the initial distribution of defects, grain boundaries can form via the mobility of individual particles. By imaging in live fish, we demonstrate that grain boundaries in the cone mosaic instead appear during initial mosaic formation, without requiring defect motion. Motivated by this observation, we show that a computational model of repulsive cell-cell interactions generates a mosaic with grain boundaries. In contrast to paradigmatic models of fate specification in mostly motionless cell packings, this study emphasizes the role of cell motion, guided by cell-cell interactions during differentiation, in forming biological crystals. Such a route to the formation of regular patterns may be especially valuable in situations, like growth on a curved surface, where long-ranged, elastic, effective interactions between defects can help to group them into grain boundaries.\n\nAUTHOR SUMMARYFrom hair cells in the mammalian inner ear to the bristles on a flys back, sensory cells often form precise arrays, ensuring that these cells are evenly spread out on the tissues surface. Here we consider the zebrafish cone mosaic, a crystal of cone photoreceptors in the outer retinal layer. Because the cone mosaic grows from the rim of the curved retinal surface, new rows of cones (i.e., defects) are inserted to maintain constant spacing between sensory cells. We study the spatial distribution of these defects to gain insight into how the cone pattern forms. By imaging retinae in live fish, we find that as differentiating cones are incorporated into the mosaic, defects form lines (grain boundaries) that separate mostly defect-free domains. Then, we show that a computational model based on repulsion between mobile cells during their incorporation into the mosaic generates similar grain boundaries. This study thus suggests that cell motion governed by repulsive cell-cell interactions can play an important role in establishing regular patterns in living systems.

biophysics↗

bioRxiv2019

Midkine-a is required for cell cycle progression of Müller glia during neuronal regeneration

In zebrafish, Muller glia function as intrinsic retinal stem cells that can regenerate ablated neurons. Understanding the mechanisms governing neuronal stem cells may provide clues to regenerate neurons in mammals. We report that in Muller glia the cytokine/growth factor, Midkine-a, functions as a core autocrine regulator of the cell cycle. Utilizing midkine-a mutants, we determined that Midkine-a regulates elements of an Id2a-retinoblastoma network in reprogrammed Muller glia that controls the expression of cell cycle genes and is required for transition from G1 to S phases of the cell cycle. In mutants, Muller glia that fail to divide undergo reactive gliosis, a pathological hallmark of Muller glia in mammals. Finally, we show that activation of the Midkine-a receptor, ALK, is required for Muller glia proliferation. These data provide mechanistic insights into Muller glia stem cells in the vertebrate retina and suggest avenues for eliciting neuronal regeneration in mammals.

developmental biology↗