Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Related Publications
• Parameters
• Instruments
• Project Information
• Funding

Methodology:
Immediately after sediment core retrieval, temperature and salinity of the water overlying sediments were measured with hand-held sensors (Orion Star A329 portable multimeter).

In the lab, surficial sediments were sectioned at 0.5 cm depth increments from which aliquots were collected for microscope enumeration of Beggiatoa-like filaments and cable bacteria filaments. Beggiatoa-like filament enumeration proceeded by methods adapted from Jorgensen et al. 2010 (doi: 10.1111/j.1574-6941.2010.00918), using inverted light microscopy (Zeiss AxioVert A1) with Utermöhl well slides. Filaments were identified as living Beggiatoa-like filaments if they were motile, unpigmented, and contained refractive sulfur granules. The length and diameter of each Beggiatoa-like filament encountered was recorded. Data are reported as volumetric density of Beggiatoa-like filaments (computed assuming a cylindrical shape), integrated to 5.0 cm depth.

To enumerate cable bacteria, cells were first detached from sediment particles using methods adapted from Kallmeyer et al. 2008, using density centrifugation with Nycodenz (50% wt/vol), and finally captured on filters (0.2 µm cellulose acetate). The identity of cable bacteria was first confirmed using fluorescent in situ hybridization (FISH) with the DSB706 oligoprobe (Schauer et al. 2014) on a subset of samples, and then enumerated following staining by Sybr Green I. A minimum of 200 randomly selected fields were viewed at 630X (Zeiss Axio Imager 2). Data are reported as cumulative length of cable bacteria filaments per volume of sediment, and as cumulative volume of cable bacteria computed assuming a cylindrical shape and cell diameter of 1 micron, each integrated to 4.0 cm depth.

For analysis of chlorophyll a (Chla) concentration in surface sediments (0-0.5 cm), pigments were extracted into 90% acetone, applying agitation by gentle sonication, and pooling 2-3 successive extractions. Pigment concentration was determined colorimetrically (ThermoScientific Evolution 60S), applying the empirical formula of (Jeffrey et al. 1975).

Sampling and Analytical Procedures:
Replicate sediment cores were collected using a gravity corer (Uwitec; clear PVC liners, Ø = 8.6 cm). Immediately after sediment core retrieval, temperature and salinity of the water overlying sediments were measured with hand-held sensors (Orion Star A329 portable multimeter). Cores were then capped, kept in the dark at bottom water temperature in a water bath, and transported back to the laboratory, where they were held in a climate-controlled room. Core sectioning was conducted within 1 day of core retrieval.

BCO-DMO Processing:
- changed date format to YYYY-MM-DD;
- converted longitude from positive degrees West to negative degrees East.

NSF Award Abstract:
Marine sediments represent the world's largest repository of stored organic carbon, and understanding how microorganisms break down this carbon is an imperative for understanding global carbon cycling. Yet long-standing questions remain regarding how networks of microorganisms work together to accomplish the complete breakdown of organic carbon in marine sediments. Sediment microbes interact in a myriad of ways that couple their metabolism to the break down of organic carbon, including by sharing products of metabolism. Accumulating evidence further suggests that some microorganisms can interact by transferring electrons directly to other unrelated microorganisms. This ability occurs across diverse microorganisms and appears to be widespread in the biosphere, particularly in anaerobic environments such as marine sediments. This project addresses emerging questions about the identity and metabolic linkages between microorganisms that work together in natural anaerobic marine and estuarine sediments to break down organic carbon. The investigators approach these questions by focusing on the influence of a keystone bacterium on its surrounding microbial community. "Cable bacteria" are a recently discovered group of long filamentous bacteria that act as electrical conductors in aquatic sediments providing a conduit for electrons to commute from deeper sulfidic sediments up to the surface oxygen layer by the process of centimeter-scale electron transport. Since their discovery about 6 years ago, these bacteria have been observed in a wide range of depositional sedimentary environments, often at extremely high cell densities. Where these bacteria are abundant, such as in coastal marine muds, they drive intense localized changes in pH and strongly influence the mineral cycling. This research explores the direct and indirect influence of cable bacteria on the metabolic activity of associated microorganisms. This project also advance the education and training of two early-career investigators, two PhD students, and undergraduate students. The skills and expertise gained from these PhD research projects will enable the students to be competitive in academic pursuits and in bioinformatics and technology applications relevant to private industry. The scientific discoveries emerging from this work is being incorporated into undergraduate and graduate level courses in marine microbial ecology. The research team will reach out to the broader community by hosting public lectures promoting a better understanding of environmental microbial ecology.

The proposed work is to investigate the role of cable bacteria in structuring sediment microbial communities. Due to their growth strategy and morphology, cable bacteria are particularly amenable to experimental manipulation, providing an outstanding opportunity to better understand community interactions among microorganisms in a natural and complex anaerobic environment. The investigators will explore the interactions and relationships between cable bacteria and their associated microbial community by manipulating the growth and activity of cable bacteria and quantifying the resultant microbial community response. Specifically, this project aims to (1) identify microorganisms whose growth is enhanced by cable bacteria, (2) identify metabolic processes linked with cable bacteria activity using metatranscriptomics, (3) test specific metabolic links between sediment microorganisms and cable bacteria activity using a DNA-stable isotope probing (SIP) approach, and (4) visually confirm the identity and quantify key microorganisms associated with cable bacteria using microscopy. As more is learned about the identity and the mechanisms by which microorganisms are metabolically linked in anoxic sediments, we will be better able to understand and make predictions about how microorganisms function in their environment and how they can be utilized in bioengineered systems.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.