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Kelly, K. H.

Publications and source records attributed to Kelly, K. H..

3 recordsLinked to original sources

Increased aridity is associated with diversity and composition changes in the biocrust mycobiome

Drylands comprise 45% of Earths land area and contain ecologically critical soil surface communities known as biocrusts. Biocrusts are composed extremotolerant organisms including cyanobacteria, microfungi, algae, lichen, and bryophytes. Fungi in biocrusts help aggregate these communities and may form symbiotic relationships with nearby plants. Climate change threatens biocrusts, particularly moss biocrusts, but its effects on the biocrust mycobiome remain unknown. Here, we performed a culture-dependent and metabarcoding survey of the moss biocrust mycobiome across an aridity gradient to determine whether local climate influences fungal community composition. As the local aridity index increased, fungal communities exhibited greater homogeneity in beta diversity. At arid and hyper-arid sites, communities shifted toward more extremotolerant taxa. We identified a significant proportion of fungal reads and cultures from biocrusts that could not be classified. Rhodotorula mucilaginosa and R. paludigena were significantly enriched following surface sterilization of healthy biocrust mosses. This aligns with their known roles as plant endophytes. We also observed septate endophyte colonization in the photosynthetic tissues of mosses from arid climates. Collectively, these results suggest that the biocrust mycobiome will undergo significant shifts in diversity due to climate change, favoring extremotolerant taxa as climate conditions intensify. The survey results also highlight taxa with the potential to serve as bioinoculants for enhancing biocrust resilience to climate change. These findings offer valuable insights into the potential impacts of climate change on drylands and provide crucial information for biocrust conservation.

microbiology↗

Novel Glomeromycotina-Moss Associations Identified in California Dryland Biocrusts

Drylands, which comprise ~45% of Earths land area, host biological soil crusts (biocrusts)--symbiotic communities of cyanobacteria, fungi, algae, lichen, and bryophytes that stabilize soil and support key ecosystem functions. Moss dominated biocrusts in particular are interesting due to their potential to illuminate ancient bryophyte-fungal interactions, but their associated microbial communities remain poorly characterized. To test the hypothesis that mosses in biocrusts harbor specific fungal associates, we conducted amplicon metabarcoding and microscopic surveys employing fungal staining across an aridity gradient. We identified novel associations between mosses and arbuscular mycorrhizal fungi (AMF), with phylogenetic analyses revealing distinct fungal communities in moss biocrusts compared to adjacent bare soil. Intracellular branching by fungi resembling Glomeromycotina was observed within healthy Trichostomopsis australaceae cells, suggesting interactions beyond saprotrophy. Moreover, shifts in AMF community composition along an aridity gradient highlight the potential vulnerability of biocrust mycobiomes to climate change. These findings provide critical insights into ancient bryophyte-fungal symbioses, potentially analogous to those enabling early land plant colonization during the Ordovician (~470 Ma). They also underscore the need to understand and protect biocrust microbial communities as aridity intensifies under climate change.

microbiology↗

Absolute abundance unveils Basidiobolus as a cross-domain bridge indirectly bolstering gut microbiome homeostasis

The host microbiome is integral to metabolism, immune function, and resilience against pathogens. However, reliance on relative abundance (RA) to estimate host-associated microbiomes introduces compositional biases, while limited tools for absolute abundance (AA) quantification hinder broader applications. To address these challenges, we developed DspikeIn (https://github.com/mghotbi/DspikeIn), an R package paired with a versatile wet-lab methodology for AA quantification. Using RA and AA to compare core microbiome distributions across herpetofauna orders and their natural histories revealed starkly distinct results, driven by aggregate effects, including inherited compositional biases in RA and additional multifactorial influences. Focusing on two closely related Desmognathus species demonstrated that AA quantification enhanced resolution in differential abundance analyses and minimized false discovery rates (FDR) when identifying enriched taxa in their gut microbiomes. Keystone taxa identified through network associations also differed between RA and AA data. For example, Lactococcus and Cetobacterium were core members in Anura and Caudata, while Basidiobolus and Mortierella were core to Chelonia and Squamata, facilitating host adaptation to diverse environments, insights undetectable with RA data. AA-based network analysis further revealed that removing the Basidiobolus subnetwork increased negative interactions, highlighting its role in promoting gut homeostasis through cross-domain connectivity. Despite low redundancy, the Basidiobolus node exhibited high betweenness, efficiency, and degree, serving as a critical bridge linking disconnected nodes or modules and indirectly supporting microbiome stability, consistent with Burts structural hole theory. DspikeIn represents a transformative tool for microbiome research, enabling the transition from RA to AA quantification and delivering more accurate, consistent, and comparable results across studies. Graphical abstract DspikeIn cheatsheet O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=156 SRC="FIGDIR/small/630554v1_ufig1.gif" ALT="Figure 1"> View larger version (65K): org.highwire.dtl.DTLVardef@150900forg.highwire.dtl.DTLVardef@21cd90org.highwire.dtl.DTLVardef@13ead1borg.highwire.dtl.DTLVardef@1d6fa84_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗