Jesse G. Dillon

Effect of environmental factors on the synthesis of scytonemin, a UV-screening pigment, in a cyanobacterium ( Chroococcidiopsis sp.)

The UV-screening pigment scytonemin is found in many species of ensheathed cyanobacteria. Past work has shown that the pigment is synthesized in response to exposure to UV-A irradiance. This study investigated the effect of other correlated stress factors including heat, osmotic and oxidative stress on the synthesis of scytonemin in a clonal cyanobacterial isolate (Chroococcidiopsis sp.) from an epilithic desert crust. Stress experiments were carried out both in conjunction with UV-A irradiance and in isolation. Increases in both temperature and photooxidative conditions in conjunction with UV-A caused a synergistic increase in the rate of scytonemin production. In contrast, increased salt concentration under UV-A irradiance inhibited scytonemin synthesis. However, unlike the responses to temperature and oxidative stress, cells synthesized low levels of scytonemin under osmotic stress in the absence of scytonemin-inducing irradiance. These results suggest that scytonemin induction may be regulated as a part of a complex stress response pathway in which multiple environmental signals affect its synthesis.

SCYTONEMIN, A CYANOBACTERIAL SHEATH PIGMENT, PROTECTS AGAINST UVC RADIATION: IMPLICATIONS FOR EARLY PHOTOSYNTHETIC LIFE

During the Precambrian, ultraviolet (UV) radiation reaching the Earth’s surface, including UVC wavelengths (190–280 nm), was considerably higher than present because of the lack of absorbing gases (e.g. O2 and O3) in the atmosphere. High UV flux would have been damaging to photosynthetic organisms exposed to solar radiation. Nevertheless, fossil evidence indicates that cyanobacteria‐like ancestors may have evolved as early as 3.5 × 109 yr ago, and were common in shallow marine habitats by 2.5 × 109 years ago. Scytonemin, a cyanobacterial extracellular sheath pigment, strongly absorbs UVC radiation. Exposure to high‐irradiance conditions caused cells to synthesize scytonemin and resulted in decreased UVC inhibition of photosynthetic carbon uptake. It was further demonstrated that scytonemin alone was sufficient for substantial protection against UVC damage. This represents the first experimental demonstration of biological protection against UVC radiation in cyanobacteria. These results suggest that scytonemin may have evolved during the Precambrian and allowed colonization of exposed, shallow‐water and terrestrial habitats by cyanobacteria or their oxygenic ancestors.

Linkage of high rates of sulfate reduction in Yellowstone hot springs to unique sequence types in the dissimilatory sulfate respiration pathway.

ABSTRACT Diversity, habitat range, and activities of sulfate-reducing prokaryotes within hot springs in Yellowstone National Park were characterized using endogenous activity measurements, molecular characterization, and enrichment. Five major phylogenetic groups were identified using PCR amplification of the dissimilatory sulfite reductase genes (dsrAB) from springs demonstrating significant sulfate reduction rates, including a warm, acidic (pH 2.5) stream and several nearly neutral hot springs with temperatures reaching 89°C. Three of these sequence groups were unrelated to named lineages, suggesting that the diversity and habitat range of sulfate-reducing prokaryotes exceeds that now represented in culture.

Spatial and temporal variability in a stratified hypersaline microbial mat community

Hypersaline microbial mat communities have recently been shown to be more diverse than once thought. The variability in community composition of hypersaline mats, both in terms of spatial and temporal dimensions, is still poorly understood. Because this information is essential to understanding the complex biotic and abiotic interactions within these communities, terminal restriction fragment analysis and 16S rRNA gene sequencing were used to characterize the near-surface community of a hypersaline microbial mat in Guerrero Negro, Mexico. Core samples were analyzed to assay community variability over large regional scales (centimeter to kilometer) and to track depth-related changes in population distribution at 250-microm intervals over a diel period. Significant changes in total species diversity were observed at increasing distances across the mat surface; however, key species (e.g. Microcoleus sp.) were identified throughout the mat. The vertical position and abundance of >50% of the 60 peaks detected varied dramatically over a diel cycle, including Beggiatoa sp., cyanobacteria, Chloroflexus sp., Halochromatium sp., Bacteroidetes sp. and several as-yet-identified bacteria. Many of these migrations correlated strongly with diel changes in redox conditions within the mat, contributing to strong day-night community structure differences.

Patterns of microbial diversity along a salinity gradient in the Guerrero Negro solar saltern, Baja CA Sur, Mexico

The goal of this study was to use environmental sequencing of 16S rRNA and bop genes to compare the diversity of planktonic bacteria and archaea across ponds with increasing salinity in the Exportadora de Sal (ESSA) evaporative saltern in Guerrero Negro, Baja CA S., Mexico. We hypothesized that diverse communities of heterotrophic bacteria and archaea would be found in the ESSA ponds, but that bacterial diversity would decrease relative to archaea at the highest salinities. Archaeal 16S rRNA diversity was higher in Ponds 11 and 12 (370 and 380 g l−1 total salts, respectively) compared to Pond 9 (180 g l−1 total salts). Both Pond 11 and 12 communities had high representation (47 and 45% of clones, respectively) by Haloquadratum walsbyi-like (99% similarity) lineages. The archaeal community in Pond 9 was dominated (79%) by a single uncultured phylotype with 99% similarity to sequences recovered from the Sfax saltern in Tunisia. This pattern was mirrored in bop gene diversity with greater numbers of highly supported phylotypes including many Haloquadratum-like sequences from the two highest salinity ponds. In Pond 9, most bop sequences, were not closely related to sequences in databases. Bacterial 16S rRNA diversity was higher than archaeal in both Pond 9 and Pond 12 samples, but not Pond 11, where a non-Salinibacter lineage within the Bacteroidetes >98% similar to environmental clones recovered from Lake Tuz in Turkey and a saltern in Chula Vista, CA was most abundant (69% of community). This OTU was also the most abundant in Pond 12, but only represented 14% of clones in the more diverse pond. The most abundant OTU in Pond 9 (33% of community) was 99% similar to an uncultured gammaproteobacterial clone from the Salton Sea. Results suggest that the communities of saltern bacteria and archaea vary even in ponds with similar salinity and further investigation into the ecology of diverse, uncultured halophile communities is warranted.

High Rates of Sulfate Reduction in a Low-Sulfate Hot Spring Microbial Mat Are Driven by a Low Level of Diversity of Sulfate-Respiring Microorganisms

ABSTRACT The importance of sulfate respiration in the microbial mat found in the low-sulfate thermal outflow of Mushroom Spring in Yellowstone National Park was evaluated using a combination of molecular, microelectrode, and radiotracer studies. Despite very low sulfate concentrations, this mat community was shown to sustain a highly active sulfur cycle. The highest rates of sulfate respiration were measured close to the surface of the mat late in the day when photosynthetic oxygen production ceased and were associated with a Thermodesulfovibrio-like population. Reduced activity at greater depths was correlated with novel populations of sulfate-reducing microorganisms, unrelated to characterized species, and most likely due to both sulfate and carbon limitation.

Seasonal changes in bacterial diversity in the Salton Sea

The Salton Sea is a large, shallow, endorheic, polymictic, saline lake in Southern California sustained by runoff from local agricultural and municipal wastewater. As a closed-basin lake in an arid region with declining water supply, it is becoming increasingly saline. Due to its eutrophic status and episodic wind-driven mixing, basin-wide anoxia events are becoming more common during summer. Sequencing of 16S rRNA gene clones obtained from the water column and sediments provided the first molecular assessment of bacterial community structure in the Salton Sea. Similar to other saline habitats, the water column community was dominated by Gamma- and Alphaproteobacteria, and Bacteroidetes, although there was significant seasonal variability in diversity, richness, and the specific genera recovered. Sediments showed high diversity and richness and were dominated by sequences from cultured and uncultured phyla typical of marine sediments, especially the Deltaproteobacteria. This study has provided baseline data about the bacterial communities found in this important California water body and may serve as important indicators of change as the lake becomes increasingly saline over time or as remediation efforts are enacted.

Lignocellulose-responsive bacteria in a southern California salt marsh identified by stable isotope probing.

Carbon cycling by microbes has been recognized as the main mechanism of organic matter decomposition and export in coastal wetlands, yet very little is known about the functional diversity of specific groups of decomposers (e.g., bacteria) in salt marsh benthic trophic structure. Indeed, salt marsh sediment bacteria remain largely in a black box in terms of their diversity and functional roles within salt marsh benthic food web pathways. We used DNA stable isotope probing (SIP) utilizing 13C-labeled lignocellulose as a proxy to evaluate the fate of macrophyte-derived carbon in benthic salt marsh bacterial communities. Overall, 146 bacterial species were detected using SIP, of which only 12 lineages were shared between enriched and non-enriched communities. Abundant groups from the 13C-labeled community included Desulfosarcina, Spirochaeta, and Kangiella. This study is the first to use heavy-labeled lignocellulose to identify bacteria responsible for macrophyte carbon utilization in salt marsh sediments and will allow future studies to target specific lineages to elucidate their role in salt marsh carbon cycling and ultimately aid our understanding of the potential of salt marshes to store carbon.

Stable Isotope Phenotyping via Cluster Analysis of NanoSIMS Data As a Method for Characterizing Distinct Microbial Ecophysiologies and Sulfur-Cycling in the Environment

Stable isotope probing (SIP) is a valuable tool for gaining insights into ecophysiology and biogeochemical cycling of environmental microbial communities by tracking isotopically labeled compounds into cellular macromolecules as well as into byproducts of respiration. SIP, in conjunction with nanoscale secondary ion mass spectrometry (NanoSIMS), allows for the visualization of isotope incorporation at the single cell level. In this manner, both active cells within a diverse population as well as heterogeneity in metabolism within a homogeneous population can be observed. The ecophysiological implications of these single cell stable isotope measurements are often limited to the taxonomic resolution of paired fluorescence in situ hybridization (FISH) microscopy. Here we introduce a taxonomy-independent method using multi-isotope SIP and NanoSIMS for identifying and grouping phenotypically similar microbial cells by their chemical and isotopic fingerprint. This method was applied to SIP experiments in a sulfur-cycling biofilm collected from sulfidic intertidal vents amended with 13C-acetate, 15N-ammonium, and 33S-sulfate. Using a cluster analysis technique based on fuzzy c-means to group cells according to their isotope (13C/12C, 15N/14N, and 33S/32S) and elemental ratio (C/CN and S/CN) profiles, our analysis partitioned ~2200 cellular regions of interest (ROIs) into five distinct groups. These isotope phenotype groupings are reflective of the variation in labeled substrate uptake by cells in a multispecies metabolic network dominated by Gamma- and Deltaproteobacteria. Populations independently grouped by isotope phenotype were subsequently compared with paired FISH data, demonstrating a single coherent deltaproteobacterial cluster and multiple gammaproteobacterial groups, highlighting the distinct ecophysiologies of spatially-associated microbes within the sulfur-cycling biofilm from White Point Beach, CA.

Diversity of Desulfobacteriaceae and Overall Activity of Sulfate-Reducing Microorganisms in and Around a Salt pan in a Southern California Coastal Wetland

Sulfate-reducing bacteria (SRB) are key mediators of anaerobic carbon cycling in coastal salt marsh sediments and have been shown to be important decomposer communities even in hypersaline habitats. Understanding how SRB function in various salt marsh habitats (vegetated, salt pans) is crucial to advancing our knowledge of salt marsh function. We compare overall sulfate reducing activity and the diversity of a subset of SRB (Desulfobacteriaceae) in two hypersaline sediments (salt pan and nearby area with desiccated vegetation) with a regularly inundated control site within the Huntington Beach Wetlands (HBW). Biological activity was quantified using radiotracer studies to measure sulfate reduction rates (SRR) with and without carbon amendment. All sites showed enhanced SRR under carbon amendment, suggesting short-term carbon limitation. Unique communities of Desulfobacteriaceae were found in all three sites with increased incidence of halotolerant genotypes in the salt pan. These findings indicate that, despite reduced anaerobic respiratory activity, highly diverse and functional deltaproteobacterial communities exist in salt pan and surrounding hypersaline habitats in coastal salt marshes in southern California.