Biology subjects

Beman, J. M.

Publications and source records attributed to Beman, J. M..

4 recordsLinked to original sources

bioRxiv2023

The microbiome of an amphibious plant shifts dramatically across the host life cycle.

Interactions between plants and their associated microbiomes are thought to enhance the capacity of the host plant to overcome extreme conditions, yet the significance of microbially mediated stress tolerance in most plant species and ecosystems remains unknown. For the first time, we examined the microbiome of the amphibious plant Eryngium castrense (Apiaceae) inhabiting Mediterranean climate ephemeral wetlands in California. Eryngium castrense has the capacity to survive as both an aquatic and terrestrial plant, thereby living under contrasting extremes of water stress. Whether plant-associated microbial communities are also affected by such changes, and what ecological role they play while inhabiting amphibious plants, is an underexplored topic of plant-microbial interactions in natural and artificial systems. We amplified and sequenced 16S rRNA genes from bacteria and archaea to examine microbial communities associated with roots and shoots over the plants full life cycle. We observed that the microbiome changes from the aquatic stage to the terrestrial stage, and that roots and shoots represent distinct habitats within the plant host ecosystem. When compared with soil and water column samples, plant samples retained a unique, differentiated core microbiome. Taxa located in the roots during the terrestrial stage were linked with potential functions such as nitrogen acquisition, sulfur assimilation, and resistance to heavy metals, whereas aquatic roots held potential phythoparasites. Overall, our results provide new insights into symbiotic relationships in plants subject to stress-related to water saturation and deficiency.

microbiology↗

bioRxiv2020

Biogeochemical and omic evidence for multiple paradoxical methane production mechanisms in freshwater lakes

Aquatic ecosystems are globally significant sources of the greenhouse gas methane (CH4) to the atmosphere. However, CH4 is produced paradoxically in oxygenated water via poorly understood mechanisms, fundamentally limiting our understanding of overall CH4 production. Here we resolve paradoxical CH4 production mechanisms through CH4 measurements,{delta} 13CH4 analyses, 16S rRNA sequencing, and metagenomics/metatranscriptomics applied to freshwater incubation experiments with multiple time points and treatments (addition of a methanogenesis inhibitor, dark, high-light). We captured significant paradoxical CH4 production, as well as consistent metabolism of methylphosphonate by abundant bacteria--resembling observations from marine ecosystems. Metatranscriptomics and{delta} 13CH4 analyses applied to experimental treatments identified an additional CH4 production mechanism associated with (bacterio)chlorophyll metabolism and photosynthesis by Cyanobacteria, and especially by Proteobacteria. Both mechanisms occured together within metagenome-assembled genomes, and appear widespread in freshwater. Our results indicate that multiple, co-occurring, and broadly-distributed bacterial groups and metabolic pathways produce CH4 in aquatic ecosystems.

genomics↗

bioRxiv2020

Constraining oxygen consumption by nitrite oxidation in oceanic oxygen minimum zones

Oceanic oxygen minimum zones (OMZs) are globally significant sites of biogeochemical cycling where microorganisms deplete dissolved oxygen (DO) to concentrations <20 {micro}M. Amid intense competition for DO in these metabolically challenging environments, aerobic nitrite oxidation may consume significant amounts of DO and help maintain low DO concentrations, but this remains unquantified. Using parallel measurements of oxygen consumption rates and 15N-nitrite oxidation rates applied to both water column profiles and oxygen manipulation experiments, we show that the contribution of nitrite oxidation to overall DO consumption systematically increases as DO declines below 2 {micro}M. Nitrite oxidation could account for all DO consumption only under DO concentrations <393 nM found in and below the secondary chlorophyll maximum. These patterns were consistent across sampling stations and experiments, reflecting coupling between nitrate reduction and nitrite-oxidizing Nitrospina with high oxygen affinity (based on isotopic and omic data). Collectively our results provide new insight into the contribution of nitrite oxidation to the maintenance and biogeochemical dynamics of OMZs.

microbiology↗

bioRxiv2018

Archaeal, bacterial, and eukaryal microbial community structure of sediment and seawater in a coastal region near Puerto Nuevo, Baja California

Microbial communities control numerous biogeochemical processes critical for ecosystem function and health, particularly in coastal ecosystems. However, comparatively little is known about microbial community structure in coastal regions, such that basic patterns of microbial biodiversity, such as species richness and community composition, are generally understudied. To better understand the global patterns of microbial biodiversity in coastal ecosystems, we characterized sediment and seawater microbial communities for three sites near Puerto Nuevo (Baja California, Mexico) using 16S and 18S rRNA gene amplicon sequencing methods. We found that sediment bacteria, archaea, and eukaryote microbial communities contained approximately 5 x 10^2 fold greater operational taxonomic units (OTUs) than their seawater-based counterparts (p < 0.001). Further, distinct bacterial, archaeal and eukaryal phyla were found in sediment and seawater samples. The phyla Acidobacteria, Chlorobi, and Chloroflexi were found to be abundant and unique to the sediment and Cyanobacteria, Spirochaetae, and Woesearchaeota to the seawater environment. Apicomplexa and Arthropoda were abundant eukaryal phyla found uniquely in the sediment whereas the Cryptomonadales and Protalveolata were detected only in the seawater. Furthermore, bacterial and archaeal communities were statistically different by site (p < 0.05) in both seawater and sediment samples for the Major Outlet site, the site closest to a residential area. In contrast, eukaryal microbial communities were only different among sites in the seawater samples. Overall, these results suggest that our understanding of coastal microbial biodiversity patterns require spatially robust sampling. This study contributes to a growing body of foundational microbial biodiversity and ecology knowledge, providing context to the global change that is induced by urban development.

microbiology↗