Biology subjects

Morris, R. M.

Publications and source records attributed to Morris, R. M..

4 recordsLinked to original sources

bioRxiv2025

Dissolved oxygen concentrations influence microbial diversity, abundance and dominant players in an oxygen minimum zone

Expansion of marine global oxygen minimum zones (OMZs) can have profound impacts on resident macrofauna. Less obvious is the influence OMZs will have on the diversity and abundance of planktonic microbes. This is particularly true in understudied OMZs such as the northern Benguela Upwelling System (nBUS). Here, we analyzed the influence of oxygen concentrations on the microbial community in the nBUS OMZ using 16S rRNA gene (iTag) sequence data. In the nBUS oxygen was a primary driver influencing microbial community structure and diversity. Diversity was highest in dysoxic samples and lowest in suboxic samples, which was primarily due to changes in community evenness in relationship to oxygen concentrations. For example, evenness decreased in suboxic samples due to oscillations in the abundance of microbial groups such as Thioglobaceae (SUP05), which was found to be the most abundant microbe in the nBUS OMZ and significantly increased in abundance as oxygen decreased. This finding prompted an analysis of 217 publicly available medium to high quality Thioglobaceae genomes, including cultured representatives, from the nBUS and other OMZs. Genome annotation of these Thioglobaceae indicated important roles in carbon cycling, sulfur oxidation and denitrification. Importantly, few Thioglobaceae possess the genetic potential to carry out complete denitrification, as most lack the gene that codes for nitrous oxide reductase (NosZ), which converts nitrous oxide (N2O), a potent greenhouse gas, to nitrogen gas. As OMZs expand in size and severity, decreasing microbial diversity and a concomitant increase in Thioglobaceae abundances, could lead to enhanced N2O production through incomplete denitrification. ImportanceHere, we found that microbial diversity decreased significantly with declining oxygen concentrations in the nBUS OMZ. However, one microbial group, the Thioglobaceae, was most abundant when oxygen was lowest. This group is able to support its growth through sulfur oxidation using either oxygen or nitrate (denitrification). A comprehensive genomic analysis of Thioglobaceae in the nBUS and in the global ocean revealed that few have the capacity to carry out complete denitrification, with the final step in this process often missing in these genomes. This incomplete pathway is consequential, as it can be an important source of nitrous oxide, particularly in marine OMZs such as the understudied nBUS. Collectively, this study provides new information on an OMZ, and definitively links an important microbial pathway, incomplete denitrification, to a particular and highly abundant group of microbes that appear to have a strong response to declining oxygen concentrations in the marine environment.

microbiology↗

bioRxiv2025

Denitrification genes in SAR11 and other ubiquitous lineages of marine bacteria isolated from the northern Benguela Upwelling System

Denitrification is a microbial process that leads to nitrogen loss from marine oxygen minimum zones (OMZs). The complete metabolic pathway for denitrification reduces nitrate to dinitrogen gas in four sequential steps. Many anaerobic and facultatively anaerobic bacteria are capable of the initial step of nitrate reduction to nitrite. Far fewer reduce nitrite to nitric oxide, nitrous oxide, or dinitrogen gas. In this study, we cultured and sequenced the complete genomes of 24 bacteria isolated from low dissolved oxygen waters (DO = 24 {micro}M) in the northern Benguela Upwelling System (nBUS) OMZ to identify facultatively anaerobic bacteria with the genetic potential to contribute to denitrification. Most of the isolates obtained from the nBUS have denitrification genes (79%). They include several new species in the order Pelagibacterales (SAR11), as well as representatives from a previously uncultured family of Arenicellales (UBA868), a previously uncultured genus of Paracoccaceae, and a previously undescribed genus of Porticoccaceae. All ten nBUS SAR11 have a previously unidentified genomic region that codes for a copper-containing nitrite reductase (nirK), suggesting that they have the potential to contribute to nitrogen loss by respiring nitrite to nitric oxide. Significance StatementVast genomic diversity has confounded sequencing efforts to identity the potential for marine bacteria to contribute to denitrification in marine oxygen minimum zones (OMZs). To identify facultatively anaerobic microbes with the genetic potential to contribute to marine nitrogen loss, we cultured and sequenced the complete genomes of bacteria from low-oxygen waters of the northern Benguela Upwelling System. Complete genomes allowed for a comprehensive analysis of denitrification. Most bacterial isolates, including all ten SAR11, have the genetic potential to contribute to denitrification. This suggests that some of the most abundant lineages of marine bacteria in the oceans are adapted to anoxic conditions in OMZs and may have a more direct role in marine nitrogen loss than previously suspected.

microbiology↗

bioRxiv2025

Marine community metabolomes in the eastern tropical North Pacific Oxygen Deficient Zone reveal glycine betaine as a metabolic link between Prochlorococcus and SAR11

Oxygen deficient zones (ODZs) are subsurface marine systems that harbor distinct microbial communities, including populations of the picocyanobacteria Prochlorococcus that can form a secondary chlorophyll maximum (SCM), and low-oxygen tolerant strains of the globally abundant heterotroph Pelagibacter (SAR11). Yet, the small labile molecules (metabolites) responsible for maintaining these ODZ communities are unknown. Here, we compared the metabolome of an ODZ to that of an oxygenated site by quantifying 87 metabolites across depth profiles in the eastern tropical North Pacific ODZ and the oxygenated waters of the North Pacific Gyre. Metabolomes were largely consistent between anoxic and oxic water columns. However, the osmolyte glycine betaine (GBT) was enriched in the oxycline and SCM of the ETNP, comprising as much as 1.2% of particulate organic carbon. Transcriptomes revealed two active GBT production pathways, glycine methylation (SDMT/bsmB) expressed by Prochlorococcus and choline oxidation (betB) expressed by Gammaproteobacteria. GBT consumption through demethylation involved diverse microbial taxa, with SAR11 contributing nearly half of the transcripts for the initial step of GBT demethylation (BHMT), which is predicted to convert GBT and homocysteine into dimethylglycine and methionine, a compound SAR11 cannot otherwise produce. Thus, GBT connects the metabolisms of the dominant phototroph and heterotroph in the oceans.

systems biology↗

bioRxiv2025

Genome restructuring and adaptation in Arctic marine bacteria

Arctic marine bacteria experience seasonal changes in temperature, salinity, and light caused by the formation and melting of sea-ice. Time-series studies have identified spatial and temporal patterns in microbial communities in the Arctic and environmental sequencing has provided insights into the genetic potential of key taxa. We cultured and sequenced the complete genomes of 34 Arctic marine bacteria to identify patterns of gene gain, loss, and rearrangement that structure genomes and underlie adaptations to Arctic conditions. We found that the most abundant lineage in the Arctic (SAR11) is comprised of diverse species and subspecies, each encoding 50-150 unique genes. Half of the SAR11 genomes (8/16) harbor a genomic island with the potential to enhance survival in the Arctic by utilizing the osmoprotectant and potential methyl donor glycine betaine. We also cultured and sequenced four species from a new family of Pseudomonadales, four subspecies of Pseudothioglobus (SUP05), a genus of high GC Puniceispirillaes (SAR116), and a family of low GC SAR116. Time-series data indicate that this collection represents up to 60% of the marine bacterial community in Arctic waters at peak abundance. Their complete genomes provide insights into the evolutionary processes that underlie diversity and adaptation to the Arctic Ocean.

microbiology↗