Browsing by Author "Biddle, Jennifer F."
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Item Archaeal blooms and busts in an estuarine time series(Environmental Microbiology, 2024-02-07) Guider, Justin T.; Yoshimura, Kristin M.; Block, Kaleigh R.; Biddle, Jennifer F.; Shah Walter. Sunita R.Coastal bays, such as Delaware Bay, are highly productive, ecologically important transitions between rivers and the coastal ocean. They offer opportunities to investigate archaeal assemblages across seasons, with the exchange of water masses that occurs with tidal cycles, and in the context of variable organic matter quality. For a year-long estuarine, size-fractionated time series, we used amplicon sequencing, chemical measurements, and qPCR to follow archaeal groups through the seasons. We detected seasonally high abundances of Marine Group II archaea in summer months which correlate with indicators of phytoplankton production, although not phytoplankton biomass. Although previous studies have reported associations between Marine Group II archaea and particles, here they are almost entirely found in very small particles (0.22–0.7 μm), suggesting they are free-living cells. Populations of Nitrososphaeria did not vary with particle size or environmental conditions. Methanogens were significant fractions of archaeal sequences in large particles at low tide during winter months. Contrary to expectations, Nanoarchaeia were found predominantly in the free-living fraction despite the previous observation that they require an association with hosts. These results underscore the utility of time series studies in shallow, tidally mixed estuarine environments that capture variable conditions for understanding the ecology and biogeochemistry of planktic archaea.Item Cultivation-dependent and cultivation-independent characterization of hydrocarbon-degrading bacteria in Guaymas Basin sediments.(Frontiers Media S.A., 2015-07-07) Gutierrez, Tony; Biddle, Jennifer F.; Teske, Andreas; Aitken, Michael D.; Tony Gutierrez, Jennifer F. Biddle, Andreas Teske and Michael D. Aitken; Biddle, Jennifer F.Marine hydrocarbon-degrading bacteria perform a fundamental role in the biodegradation of crude oil and its petrochemical derivatives in coastal and open ocean environments. However, there is a paucity of knowledge on the diversity and function of these organisms in deep-sea sediment. Here we used stable-isotope probing (SIP), a valuable tool to link the phylogeny and function of targeted microbial groups, to investigate polycyclic aromatic hydrocarbon (PAH)-degrading bacteria under aerobic conditions in sediments from Guaymas Basin with uniformly labeled [(13)C]-phenanthrene (PHE). The dominant sequences in clone libraries constructed from (13)C-enriched bacterial DNA (from PHE enrichments) were identified to belong to the genus Cycloclasticus. We used quantitative PCR primers targeting the 16S rRNA gene of the SIP-identified Cycloclasticus to determine their abundance in sediment incubations amended with unlabeled PHE and showed substantial increases in gene abundance during the experiments. We also isolated a strain, BG-2, representing the SIP-identified Cycloclasticus sequence (99.9% 16S rRNA gene sequence identity), and used this strain to provide direct evidence of PHE degradation and mineralization. In addition, we isolated Halomonas, Thalassospira, and Lutibacterium sp. with demonstrable PHE-degrading capacity from Guaymas Basin sediment. This study demonstrates the value of coupling SIP with cultivation methods to identify and expand on the known diversity of PAH-degrading bacteria in the deep-sea.Item High methane concentrations in tidal salt marsh soils: Where does the methane go?(Global Change Biology, 2023-11-30) Capooci, Margaret; Seyfferth, Angelia L.; Tobias, Craig; Wozniak, Andrew S.; Hedgpeth, Alexandra; Bowen, Malique; Biddle, Jennifer F.; McFarlane, Karis J.; Vargas, RodrigoTidal salt marshes produce and emit CH4. Therefore, it is critical to understand the biogeochemical controls that regulate CH4 spatial and temporal dynamics in wetlands. The prevailing paradigm assumes that acetoclastic methanogenesis is the dominant pathway for CH4 production, and higher salinity concentrations inhibit CH4 production in salt marshes. Recent evidence shows that CH4 is produced within salt marshes via methylotrophic methanogenesis, a process not inhibited by sulfate reduction. To further explore this conundrum, we performed measurements of soil–atmosphere CH4 and CO2 fluxes coupled with depth profiles of soil CH4 and CO2 pore water gas concentrations, stable and radioisotopes, pore water chemistry, and microbial community composition to assess CH4 production and fate within a temperate tidal salt marsh. We found unexpectedly high CH4 concentrations up to 145,000 μmol mol−1 positively correlated with S2− (salinity range: 6.6–14.5 ppt). Despite large CH4 production within the soil, soil–atmosphere CH4 fluxes were low but with higher emissions and extreme variability during plant senescence (84.3 ± 684.4 nmol m−2 s−1). CH4 and CO2 within the soil pore water were produced from young carbon, with most Δ14C-CH4 and Δ14C-CO2 values at or above modern. We found evidence that CH4 within soils was produced by methylotrophic and hydrogenotrophic methanogenesis. Several pathways exist after CH4 is produced, including diffusion into the atmosphere, CH4 oxidation, and lateral export to adjacent tidal creeks; the latter being the most likely dominant flux. Our findings demonstrate that CH4 production and fluxes are biogeochemically heterogeneous, with multiple processes and pathways that can co-occur and vary in importance over the year. This study highlights the potential for high CH4 production, the need to understand the underlying biogeochemical controls, and the challenges of evaluating CH4 budgets and blue carbon in salt marshes.Item Microbial Communities in Methane- and Short Chain Alkane-Rich Hydrothermal Sediments of Guaymas Basin(Frontiers Media SA, 2016-01-29) Dowell, Frederick; Cardman, Zena; Dasarathy, Srishti; Kellermann, MatthiasY.; Lipp, Julius S.; Ruff, S. Emil; Biddle, Jennifer F.; McKay, Luke J.; MacGregor, Barbara J.; Lloyd, Karen G.; Albert, Daniel B.; Mendlovitz, Howard; Hinrichs, Kai-Uwe; Teske, Andreas; Frederick Dowell, Zena Cardman, Srishti Dasarathy, Matthias Y. Kellermann, Julius S. Lipp, S. Emil Ruff, Jennifer F. Biddle, Luke J. McKay, Barbara J. MacGregor, Karen G. Lloyd, Daniel B. Albert, Howard Mendlovitz, Kai-Uwe Hinrichs and Andreas Teske; Biddle, Jennifer F.The hydrothermal sediments of Guaymas Basin, an active spreading center in the Gulf of California (Mexico), are rich in porewater methane, short-chain alkanes, sulfate and sulfide, and provide a model system to explore habitat preferences of microorganisms, including sulfate-dependent, methane- and short chain alkane-oxidizing microbial communities. In this study, hot sediments (above 60°C) covered with sulfur-oxidizing microbial mats surrounding a hydrothermal mound (termed “Mat Mound”) were characterized by porewater geochemistry of methane, C2–C6 short-chain alkanes, sulfate, sulfide, sulfate reduction rate measurements, in situ temperature gradients, bacterial and archaeal 16S rRNA gene clone libraries and V6 tag pyrosequencing. The most abundantly detected groups in the Mat mound sediments include anaerobic methane-oxidizing archaea of the ANME-1 lineage and its sister clade ANME-1Guaymas, the uncultured bacterial groups SEEP-SRB2 within the Deltaproteobacteria and the separately branching HotSeep-1 Group; these uncultured bacteria are candidates for sulfate-reducing alkane oxidation and for sulfate-reducing syntrophy with ANME archaea. The archaeal dataset indicates distinct habitat preferences for ANME-1, ANME-1-Guaymas, and ANME-2 archaea in Guaymas Basin hydrothermal sediments. The bacterial groups SEEP-SRB2 and HotSeep-1 co-occur with ANME-1 and ANME-1Guaymas in hydrothermally active sediments underneath microbial mats in Guaymas Basin. We propose the working hypothesis that this mixed bacterial and archaeal community catalyzes the oxidation of both methane and short-chain alkanes, and constitutes a microbial community signature that is characteristic for hydrothermal and/or cold seep sediments containing both substrates.Item Occurrence, Diversity, and Genomes of “Candidatus Patescibacteria” along the Early Diagenesis of Marine Sediments(Applied and Environmental Microbiology, 2022-12-05) Zhao, Rui; Farag, Ibrahim F.; Jørgensen, Steffen L.; Biddle, Jennifer F.The phylum “Candidatus Patescibacteria” (or Candidate Phyla Radiation [CPR]) accounts for roughly one-quarter of microbial diversity on Earth, but the presence and diversity of these bacteria in marine sediments have been rarely charted. Here, we investigate the abundance, diversity, and metabolic capacities of CPR bacteria in three sediment sites (Mohns Ridge, North Pond, and Costa Rica Margin) with samples covering a wide range of redox zones formed during the early diagenesis of organic matter. Through metagenome sequencing, we found that all investigated sediment horizons contain “Ca. Patescibacteria” (0.4 to 28% of the total communities), which are affiliated with the classes “Ca. Paceibacteria,” “Ca. Gracilibacteria,” “Ca. Microgenomatia,” “Ca. Saccharimonadia,” “Ca. ABY1,” and “Ca. WWE3.” However, only a subset of the diversity of marine sediment “Ca. Patescibacteria,” especially the classes “Ca. Paceibacteria” and “Ca. Gracilibacteria,” can be captured by 16S rRNA gene amplicon sequencing with commonly used universal primers. We recovered 11 metagenome-assembled genomes (MAGs) of CPR from these sediments, most of which are novel at the family or genus level in the “Ca. Paceibacteria” class and are missed by the amplicon sequencing. While individual MAGs are confined to specific anoxic niches, the lack of capacities to utilize the prevailing terminal electron acceptors indicates that they may not be directly selected by the local redox conditions. These CPR bacteria lack essential biosynthesis pathways and may use a truncated glycolysis pathway to conserve energy as fermentative organotrophs. Our findings suggest that marine sediments harbor some novel yet widespread CPR bacteria during the early diagenesis of organic matter, which needs to be considered in population dynamics assessments in this vast environment. IMPORTANCE Ultrasmall-celled “Ca. Patescibacteria” have been estimated to account for one-quarter of the total microbial diversity on Earth, the parasitic lifestyle of which may exert a profound control on the overall microbial population size of the local ecosystems. However, their diversity and metabolic functions in marine sediments, one of the largest yet understudied ecosystems on Earth, remain virtually uncharacterized. By applying cultivation-independent approaches to a range of sediment redox zones, we reveal that “Ca. Patescibacteria” members are rare but widespread regardless of the prevailing geochemical conditions. These bacteria are affiliated with novel branches of “Ca. Patescibacteria” and have been largely missed in marker gene-based surveys. They do not have respiration capacity but may conserve energy by fermenting organic compounds from their episymbiotic hosts. Our findings suggest that these novel “Ca. Patescibacteria” are among the previously overlooked microbes in diverse marine sediments.Item “Sifarchaeota,” a Novel Asgard Phylum from Costa Rican Sediment Capable of Polysaccharide Degradation and Anaerobic Methylotrophy(Applied and Environmental Microbiology, 2021-02-19) Farag, Ibrahim F.; Zhao, Rui; Biddle, Jennifer F.The Asgard superphylum is a deeply branching monophyletic group of Archaea, recently described as some of the closest relatives of the eukaryotic ancestor. The wide application of genomic analyses from metagenome sequencing has established six distinct phyla, whose genomes encode diverse metabolic capacities and which play important biogeochemical and ecological roles in marine sediments. Here, we describe two metagenome-assembled genomes (MAGs) recovered from deep marine sediments off the Costa Rica margin, defining a novel lineage phylogenetically married to “Candidatus Thorarchaeota”; as such, we propose the name “Sifarchaeota” for this phylum. The two Sifarchaeota MAGs encode an anaerobic pathway for methylotrophy enabling the utilization of C1 to C3 compounds (methanol and methylamines) to synthesize acetyl coenzyme A (acetyl-CoA). The MAGs showed a remarkable saccharolytic capabilities compared to other Asgard lineages and encoded diverse classes of carbohydrate active enzymes (CAZymes) targeting different mono-, di-, and oligosaccharides. Comparative genomic analysis based on the full metabolic profiles of different Asgard lineages revealed the close relation between Sifarchaeota and “Candidatus Odinarchaeota” MAGs, which suggested similar metabolic potentials and ecological roles. Furthermore, we identified multiple HGT events from different bacterial donors within Sifarchaeota MAGs, which hypothetically expanded Sifarchaeota capacities for substrate utilization, energy production, and niche adaptation.