Robert E. Hodson

Bacterial carbon processing by generalist species in the coastal ocean

The assimilation and mineralization of dissolved organic carbon (DOC) by marine bacterioplankton is a major process in the ocean carbon cycle. However, little information exists on the specific metabolic functions of participating bacteria and on whether individual taxa specialize on particular components of the marine DOC pool. Here we use experimental metagenomics to show that coastal communities are populated by taxa capable of metabolizing a wide variety of organic carbon compounds. Genomic DNA captured from bacterial community subsets metabolizing a single model component of the DOC pool (either dimethylsulphoniopropionate or vanillate) showed substantial overlap in gene composition as well as a diversity of carbon-processing capabilities beyond the selected phenotypes. Our direct measure of niche breadth for bacterial functional assemblages indicates that, in accordance with ecological theory, heterogeneity in the composition and supply of organic carbon to coastal oceans may favour generalist bacteria. In the important interplay between microbial community structure and biogeochemical cycling, coastal heterotrophic communities may be controlled less by transient changes in the carbon reservoir that they process and more by factors such as trophic interactions and physical conditions.

Application of digital image analysis and flow cytometry to enumerate marine viruses stained with SYBR gold.

ABSTRACT A novel nucleic acid stain, SYBR Gold, was used to stain marine viral particles in various types of samples. Viral particles stained with SYBR Gold yielded bright and stable fluorescent signals that could be detected by a cooled charge-coupled device camera or by flow cytometry. The fluorescent signal strength of SYBR Gold-stained viruses was about twice that of SYBR Green I-stained viruses. Digital images of SYBR Gold-stained viral particles were processed to enumerate the concentration of viral particles by using digital image analysis software. Estimates of viral concentration based on digitized images were 1.3 times higher than those based on direct counting by epifluorescence microscopy. Direct epifluorescence counts of SYBR Gold-stained viral particles were in turn about 1.34 times higher than those estimated by the transmission electron microscope method. Bacteriophage lysates stained with SYBR Gold formed a distinct population in flow cytometric signatures. Flow cytometric analysis revealed at least four viral subpopulations for a Lake Erie sample and two subpopulations for a Georgia coastal sample. Flow cytometry-based viral counts for various types of samples averaged 1.1 times higher than direct epifluorescence microscopic counts. The potential application of digital image analysis and flow cytometry for rapid and accurate measurement of viral abundance in aquatic environments is discussed.

Terrestrial inputs of organic matter to coastal ecosystems: An intercomparison of chemical characteristics and bioavailability

Dissolved and particulate organic matter (DOM and POM) collected from rivers or groundwater feeding five estuaries along the east and west coasts of the USA were characterized with a variety of biogeochemical techniques and related to bioavailability to estuarine microbes. Surface water was sampled from the Columbia, Satilla, Susquehanna and Parker Rivers and groundwater was sampled from the Childs River. Several geochemical descriptors (percent organic matter of suspended particulate matter, C/N, lignin phenol content, ratio of vanillic acid to vanillin) suggested an ordering of the systems with respect to POM lability: Satilla < Parker < Columbia < Susquehanna.DOC concentrations in these systems ranged from <100 μM for the Columbia River to >2000 μM for the Satilla River. Elemental analysis of DOM concentrates (>1000 D) was used to predict organic matter composition and to calculate degree of substrate reduction using two different modeling approaches. Models predicted aliphatic carbon ranging between 43 and 60% and aromatic carbon between 26 and 36%, with aliphatic content lowest in the Satilla and highest in the Columbia River. The degree of substrate reduction of the organic matter concentrates followed a pattern similar to that for aliphatic C, being lowest in the Satilla (3.5) and highest in the Columbia (4.0). Extracellular enzyme activity varied broadly across the systems, but again ordered sites in the same way as did aliphatic content and degree of substrate reduction. Bacterial growth rates ranged from 1.3 ug mg-1 d-1 DOC in the Satilla to 1.7 ug mg-1 d-1 DOC in the Parker River. Bioassays confirmed patterns of dissolved organic matter lability predicted by the chemical models. Between 67% to 75% of the variation in bacterial growth could be explained by differences in organic matter composition.

Phylogenetic Diversity of Marine Cyanophage Isolates and Natural Virus Communities as Revealed by Sequences of Viral Capsid Assembly Protein Gene g20

ABSTRACT In order to characterize the genetic diversity and phylogenetic affiliations of marine cyanophage isolates and natural cyanophage assemblages, oligonucleotide primers CPS1 and CPS8 were designed to specifically amplify ca. 592-bp fragments of the gene for viral capsid assembly protein g20. Phylogenetic analysis of isolated cyanophages revealed that the marine cyanophages were highly diverse yet more closely related to each other than to enteric coliphage T4. Genetically related marine cyanophage isolates were widely distributed without significant geographic segregation (i.e., no correlation between genetic variation and geographic distance). Cloning and sequencing analysis of six natural virus concentrates from estuarine and oligotrophic offshore environments revealed nine phylogenetic groups in a total of 114 different g20 homologs, with up to six clusters and 29 genotypes encountered in a single sample. The composition and structure of natural cyanophage communities in the estuary and open-ocean samples were different from each other, with unique phylogenetic clusters found for each environment. Changes in clonal diversity were also observed from the surface waters to the deep chlorophyll maximum layer in the open ocean. Only three clusters contained known cyanophage isolates, while the identities of the other six clusters remain unknown. Whether or not these unidentified groups are composed of bacteriophages that infect different Synechococcus groups or other closely related cyanobacteria remains to be determined. The high genetic diversity of marine cyanophage assemblages revealed by the g20 sequences suggests that marine viruses can potentially play important roles in regulating microbial genetic diversity.

Distribution, Isolation, Host Specificity, and Diversity of Cyanophages Infecting Marine Synechococcus spp. in River Estuaries

ABSTRACT The abundance of cyanophages infecting marineSynechococcus spp. increased with increasing salinity in three Georgia coastal rivers. About 80% of the cyanophage isolates were cyanomyoviruses. High cross-infectivity was found among the cyanophages infecting phycoerythrin-containingSynechococcus strains. Cyanophages in the river estuaries were diverse in terms of their morphotypes and genotypes.

Microbial utilization of dissolved organic matter from leaves of the red mangrove, Rhizophora mangle, in the Fresh Creek estuary, Bahamas

Abstract Dissolved organic matter was leached from [ 14 C]labeled leaves of the red mangrove, Rhizophora mangle , and used in studies to determine the rates and efficiencies of microbial utilization of the water-soluble components of mangrove leaves in the Fresh Creek estuary, Bahamas. Rates of microbial utilization (assimilation plus mineralization) of mangrove leachate ranged from 0·022 to 4·675 μg ml −1 h −1 depending on the concentration of leachate and the size or diversity of microbial populations. Microflora associated with decaying mangrove leaves utilized mangrove leachate at rates up to 18-fold higher than rates of leachate utilization by planktonic microflora. Chemical analyses indicated that tannins and other potentially inhibitory phenolic compounds made up a major fraction (18%) of the dissolved organic matter in mangrove leachate. Mangrove leachate did not appear to be inhibitory to the microbial uptake of leachate or the microbial degradation of the lignocellulosic component of mangrove leaves except at high concentrations (mg ml −1 ). The availability of molecular oxygen also was an important parameter affecting rates of leachate utilization; rates of microbial utilization of leachate were up to 8-fold higher under aerobic rather than anaerobic conditions. The overall efficiency of conversion of mangrove leachate into microbial biomass was high and ranged from 64% to 94%. As much as 42% of the added leachate was utilized during 2 to 12 h incubations, indicating that a major fraction of the leachable material from mangrove leaves is incorporated into microbial biomass, and thus available to animals in the estuarine food web.

Acid-Base Properties of Dissolved Organic Matter in the Estuarine Waters of Georgia, USA

The contribution of dissolved organic matter (DOM) to alkalinity in estuarine waters and its relationship to CO2 chemistry has not received much previous attention. In this paper, we present some of the first organic alkalinity measurements in the context of estuarine mixing, focusing on three rivers in the Southeastern US. The simple model presented here illustrates that the organic contribution to alkalinity in estuarine waters is largely controlled by the dramatic pH change in the early stage of the mixing. As mixing progresses, organic alkalinity becomes nearly conservative with respect to salinity change. Although no DOM removal during estuarine mixing was detected here, this work provides an alternative approach to evaluate the issues of colloid and small particle formation and coagulation during mixing. This paper demonstrates that a large fraction of the proton binding sites of humic substances is either completely protonated or deprotonated during the estuarine mixing processes and, therefore, that these sites contribute neither to alkalinity nor to proton transfer reactions. One class of chargeable sites may be adequate to model the acid-base properties of humic substances during the mixing process.

Variability in the distribution of lipid biomarkers and their molecular isotopic composition in Altamaha estuarine sediments : implications for the relative contribution of organic matter from various sources

The estuarine mixing zone is an effective trap for particulate and dissolved organic matter from many sources, and thus greatly affects transport and deposition of organic matter between the land and ocean. This study examined sedimentary distributions of various fatty acids and their stable isotope compositions at three sites which represent different levels of mixing in the Altamaha River estuary, Georgia, USA. Distributions of other neutral lipids (phytol, C14–C32 fatty alcohols, and two sterols) were also determined as supplementary biomarkers from various sources. Results suggest that POM from terrestrial plant material was dominant at an initial, upper estuary mixing zone (salinity in the water column is near zero but porewater in the sediment is saline) while POM from marine sources was mainly deposited at a more intensive mixing zone (wherein salinity in surface and bottom waters was identical) in the Altamaha. Much less particulate lipid was deposited in Altamaha River mouth sediments even during the high discharge season, suggesting that terrestrial plant-derived POM may not be significantly transported across the mixing zone. Analyses of fatty acid isotopic composition further verify the differential deposition pattern of POM from different sources.

Dissolved adenosine triphosphate utilization by free-living and attached bacterioplankton

We determined concentrations of dissolved adenosine triphosphate (DATP) and rates of its uptake by marine bacteria in seawater from the continental shelf and Gulf Stream off the southeastern USA. Dissolved adenosine triphosphate (DATP) concentrations (22 to 568 ng l−1) were highest in nearshore surface waters and at the interfaces of continental shelf water and upwelled water from the cold wall of the Gulf Stream; lowest concentrations were found in surface water furthest from shore and in subsurface waters. Bacterial population density and DATP uptake velocities were determined to calculate average rates of DATP uptake per-cell. In general, percell rates of uptake were highest in samples having the highest in situ concentrations of DATP and varied markedly with small-scale temporal and spatial changes. Per-cell uptake by attached bacteria was one to two orders of magnitude faster than uptake by free-living bacteria; this difference could be accounted for by the much larger average cell volume of the former.

Lignocellulose and lignin in the salt marsh grass Spartina alterniflora: initial concentrations and short-term, post-depositional changes in detrital matter

Lignocellulose was found to comprise the bulk of various anatomical structures of the salt marsh grass Spartina alterniflora, as well as of detritus derived from this plant; although concentrations of both lignin and lignocellulose varied with plant height-form, age, and anatomical structure. Changes in the relative concentrations of lignin and polysaccharide in lignocellulose due to long-term degradation by natural marsh microflora were determined using standard gravimetric assay procedures and a new procedure utilizing specifically-radiolabelled 14C-(cellulose)-lignocellulose and 14C-(lignin)-lignocellulose prepared from S. alterniflora. Results obtained with the two methods agreed, thus validating the new procedures. Mineralization of the cellulose moiety was more rapid than mineralization of the lignin moiety resulting in relative enrichment of S. alterniflora detritus in lignin. Rates of mineralization of both moieties decreased over time such that extent of mineralization was a function of the logarithm of aging time.