The Influence of Microbial Communities on Spatiotemporal Elemental Cycling in Coastal Margins Revealed by Community- and Population-level Genomics and Proteomics

Biotic and abiotic processes at continent-ocean interfaces cycle a disproportionate mass of carbon and nutrients relative to their global surface area, and microbial activity is a principal determinant of organic and inorganic matter flux in these transition zones. Most studies using modern high-throughput ‘omics techniques to link microorganisms with costal biogeochemical cycles have focused on large riverine-estuarine continuums, yet there is emerging evidence that smaller, more numerous rivers and estuaries are also key contributors to regional element fluxes, especially in temperate ecosystems. In this work, I characterized microbe-mediated carbon and nutrient flux through an estuary in the highly-productive Oregon coastal margin. To achieve this aim, I used multiple ‘omics techniques to characterize the functional and taxonomic composition, diversity, and activity of estuarine and coastal microorganisms at the community and population levels and across ecologically- relevant spatial scales. Chapter 2 presents the first spatially-resolved effort to measure microbial metabolic capacity for altering carbon and nitrogen flowing from the Yaquina River to the coastal ocean. Overall, we concluded that the microbial activity in Yaquina Bay is (1) a net source of carbon dioxide to the atmosphere via a biased capacity for respiratory processes and (spatially-constrained) carbon monoxide oxidation, and (2) a net sink of inorganic nitrogen via imbalanced assimilation and mineralization potentials. Population-level life strategies of microbial groups were also important for carbon and nitrogen cycling, with high and low molecular weight organic matter specialization divided between two dominant lineages within this system. These results represent a significant step toward constraining the flow of carbon and nitrogen through estuaries and provide future avenues of research for linking microbial populations with the specific pools of bioavailable resources. Chapter 3 describes the first investigation of microbial community composition across a winter freshwater plume on the Oregon coast. Using population distributions across space from the coastline to the continental shelf, we identified many coastal populations that may be directly involved in the turnover of plume-derived particulate organic carbon and inorganic nutrients. When these data were considered with the observations that (1) community respiration rate peaked at the plume particle maximum and (2) high concentrations of resources were ejected to the coastal ocean in plume water, we concluded that winter river plumes supplement food webs during the cold and wet season of low primary productivity on the central Oregon coast. Chapter 4 characterizes the metabolic roles of microorganisms in transforming organic matter in the Oregon coastal margin. In this project, we performed proteomic stable isotope probing (SIP) on native Yaquina Bay microbial communities using 13Carbon-labeled substrates that simulate naturally-occurring organic matter inputs from active phytoplankton into the heterotrophic food web. SIP patterns and estimated growth rates showed that these resources were partitioned among distinct bacterial taxa and assimilated by populations in taxon-specific patterns. Highly enriched community metaproteomes indicated that substrate addition primarily elicited the de novo synthesis of growth, transcription, and translation functions. Altogether, results from these experiments suggested that rapid (< 18 hours) assimilation into the biomass of many estuarine populations is a major fate of complex dissolved organic matter in Yaquina Bay, thereby making this resource available to different components of the food web in this system. A major outcome of my dissertation is the generation and interpretation of multiple datasets that help advance our understanding of microbe-mediated carbon and nutrient cycling within the Oregon coastal margin. This work is a significant contribution to the scientific community, particularly to biological oceanographers, ecosystem modelers, and microbial ecologists, by providing a prototype investigation of a small estuarine ecosystem and adjacent coastal ocean through microbiological, biogeochemical, and spatial ecology lenses, which can be extended to similar systems to constrain the role of microbes in altering carbon and nutrient flow from the land to the seas

Scholarly Societies, Scholarly Publishing, and the New Information Ecology

Since the founding of the Royal Society in the 1660s and with the development of disciplinary fields in the later nineteenth century, scholarly societies have established themselves as mediators of the professional lives of faculty and as vital components of the ecology of scholarly communication. In their interactions with libraries, societies may appear primarily as publishers of newsletters, books, reports, journals, indexes, and databases, but they also promote the creation and diffusion of knowledge by serving as hubs for professional activity, contributors to the making of public policy and opinion, providers of education, representatives of the interests of their members, and, more generally, shapers of the institutions and purposes of higher education. Society operations and education or outreach programs depend to varying degrees on revenues from publishing programs and membership dues. Today, however, changing demographics and membership decline, the academic job market, the weakening of library budgets, new modes of publishing and media for establishing scholarly reputation, and the importance of making scholarship available to a broader audience than those who can afford to purchase it challenge traditional society roles and especially the business models that have supported those roles . This paper addresses the ways in which scholarly societies are addressing the current information environment and how societies are adjusting programs and roles as they continue to build and maintain communities of scholars and promote the interests of teaching, learning, and research

Virus and Potential Host Microbes from Viral-Enriched Metagenomic Characterization in the High-Altitude Wetland, Salar de Huasco, Chile

Salar de Huasco is a wetland in the Andes mountains, located 3800 m above sea level at the Chilean Altiplano. Here we present a study aimed at characterizing the viral fraction and the microbial communities through metagenomic analysis. Two ponds (H0 and H3) were examined in November 2015. Water samples were processed using tangential flow filtration to obtain metagenomes from which the DNA fraction of the sample was amplified and sequenced (HiSeq system, Illumina). The ponds were characterized by freshwater and the viral-like particles to picoplankton ratio was 12.1 and 2.3 for H0 and H3, respectively. A great number of unassigned viral sequences were found in H0 (55.8%) and H3 (32.8%), followed by the family Fuselloviridae 20.8% (H0) and other less relatively abundant groups such as Microviridae (H0, 11.7% and H3, 3.3%) and Inoviridae (H3, 2.7%). The dominant viral sequences in both metagenomes belong to the order Caudovirales, with Siphoviridae being the most important family, especially in H3 (32.7%). The most important bacteria phyla were Proteobacteria, Bacteroidetes and Firmicutes in both sites, followed by Cyanobacteria (H0). Genes encoding lysogenic and lytic enzymes (i.e., recombinases and integrases) were found in H0 and H3, indicating a potential for active viral replication at the time of sampling; this was supported by the presence of viral metabolic auxiliary genes at both sites (e.g., cysteine hydrolase). In total, our study indicates a great novelty of viral groups, differences in taxonomic diversity and replication pathways between sites, which contribute to a better understanding of how viruses balance the cycling of energy and matter in this extreme environment.Other UBCNon UBCReviewedFacult

Metagenome-Assembled Genomes for “Candidatus Phormidium sp. Strain AB48” and Co-occurring Microorganisms from an Industrial Photobioreactor Environment

Here, we report metagenome-assembled genomes for "Candidatus Phormidium sp. strain AB48" and three cooccurring microorganisms from a biofilm-forming industrial photobioreactor environment, using the PacBio sequencing platform. Several mobile genetic elements, including a double-stranded DNA phage and plasmids, were also recovered, with the potential to mediate gene transfer within the biofilm community

Corrigendum: The survivor strain: Isolation and characterization of Phormidium yuhuli AB48, a filamentous phototactic cyanobacterium with biotechnological potential

[This corrects the article DOI: 10.3389/fbioe.2022.932695.]

Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater

Anaerobic digestion of municipal mixed sludge produces methane that can be converted into renewable natural gas. To improve economics of this microbial mediated process, metabolic interactions catalyzing biomass conversion to energy need to be identified. Here, we present a two-year time series associating microbial metabolism and physicochemistry in a full-scale wastewater treatment plant. By creating a co-occurrence network with thousands of time-resolved microbial populations from over 100 samples spanning four operating configurations, known and novel microbial consortia with potential to drive methane production were identified. Interactions between these populations were further resolved in relation to specific process configurations by mapping metagenome assembled genomes and cognate gene expression data onto the network. Prominent interactions included transcriptionally active Methanolinea methanogens and syntrophic benzoate oxidizing Syntrophorhabdus, as well as a Methanoregulaceae population and putative syntrophic acetate oxidizing bacteria affiliated with Bateroidetes (Tenuifilaceae) expressing the glycine cleavage bypass of the Wood-Ljungdahl pathway

Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater

Abstract Anaerobic digestion of municipal mixed sludge produces methane that can be converted into renewable natural gas. To improve economics of this microbial mediated process, metabolic interactions catalyzing biomass conversion to energy need to be identified. Here, we present a two-year time series associating microbial metabolism and physicochemistry in a full-scale wastewater treatment plant. By creating a co-occurrence network with thousands of time-resolved microbial populations from over 100 samples spanning four operating configurations, known and novel microbial consortia with potential to drive methane production were identified. Interactions between these populations were further resolved in relation to specific process configurations by mapping metagenome assembled genomes and cognate gene expression data onto the network. Prominent interactions included transcriptionally active Methanolinea methanogens and syntrophic benzoate oxidizing Syntrophorhabdus, as well as a Methanoregulaceae population and putative syntrophic acetate oxidizing bacteria affiliated with Bateroidetes (Tenuifilaceae) expressing the glycine cleavage bypass of the Wood–Ljungdahl pathway

Complete Genome Sequence of Phormidium yuhuli AB48, Isolated from an Industrial Photobioreactor Environment

We report the genome of Phormidium yuhuli AB48, which includes a circular chromosome and a circular plasmid (4,747,469 bp and 51,599 bp, respectively). This is currently the only closed reference genome of an isolate of the Phormidium genus, based on the Genome Taxonomy Database (GTDB), providing a potential model system for sustainable biotechnology innovation

Microbial Community Structure–Function Relationships in Yaquina Bay Estuary Reveal Spatially Distinct Carbon and Nitrogen Cycling Capacities

Linking microbial community structure to ecological processes requires understanding of the functional roles among individual populations and the factors that influence their distributions. These structure–function relationships are particularly difficult to disentangle in estuaries, due to highly variable physico-chemical conditions. Yet, examining microbe-mediated turnover of resources in these “bioreactor” ecosystems is critical for understanding estuarine ecology. In this study, a combined metagenomics and metaproteomics approach was used to show that the unequal distribution of microbial populations across the Yaquina Bay estuary led to a habitat-specific taxonomic and functional structure and a clear spatial distribution in microbe-mediated capacities for cycling of carbon and nitrogen. For example, size-fractionation revealed that communities inhabiting suspended particulate material encoded more diverse types of metabolisms (e.g., fermentation and denitrification) than those with a planktonic lifestyle, suggesting that the metabolic reactions can differ between size fractions of the same parcel of an estuarine water column. Similarly, communities inhabiting oligotrophic conditions in the lower estuary were enriched in genes involved in central carbon metabolism (e.g., TCA cycle), while communities in the upper estuary were enriched in genes typical of copiotrophic populations (e.g., cell growth, cell division). Integrating gene and protein data revealed that abundant populations of Flavobacteriales and Rhodobacterales encoded similar genomic functions, yet differed significantly in protein expression, dedicating a large proportion of their respective proteomes to rapid growth and division versus metabolic versatility and resource acquisition. This suggested potentially distinct life-strategies between these two co-occurring lineages and was concomitant with differing patterns of positive evolutionary selection on their encoded genes. Microbial communities and their functions across Yaquina Bay appear to be structured by population-level habitat preferences, resulting in spatially distinct elemental cycling, while within each community, forces such as competitive exclusion and evolutionary selection influence species life-strategies and may help maintain microbial diversity