High-throughput culturing (HTC) consisting of extinction culturing in autoclaved seawater has led to the isolation and characterization of many novel strains of oligotrophic marine bacteria. Strain HTCC 2207 was isolated from the Oregon coast by the HTC method. Phylogenetic analysis based on 16S rRNA gene sequence showed that this strain...
Candidatus Pelagibacter ubique is the first cultured representative of the SAR11 clade, a clade that is found throughout the oceans and accounts for approximately 25% of all bacterial cells [1]. It has a streamlined genome that is the smallest of any known free-living organism. In this study the complete genome...
To identify factors limiting 'Candidatus Pelagibacter ubique' maximum cell density and growth rate in pure culture on seawater, the genome sequence of 'Cand. P. ubique' was analyzed, culturing experiments with organic and inorganic nutrient additions were made, and radiotracer uptake experiments were performed. The genome was sequenced, custom data mining...
Oceanic crust covers nearly 70% of the Earth's surface, of which, the upper,
sediment layer is estimated to harbor substantial microbial biomass. Marine crust;
however, extends several kilometers beyond this surficial layer, and includes the
basalt and gabbro layers. In particular, the basalt layer has high permeabilities which
allows for...
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Figure 2.1. Overview of the Bacteria and Archaea associated with marine basalts
Proteins are the metabolic machines of the cell and as such, the study of proteins could illuminate the dominant biological activities that are occurring within cells and reveal how an organism interacts with its environment. Here, we used proteomic techniques to study the abundant marine bacterium SAR11 both as an...
A series of experiments was performed to determine the feasibility of genomic
DNA-based methods for ecological and physiological studies of dominant bacteria from
complex natural systems. Two approaches, bacterial chromosomal painting (BCP) and
environmental genomics (EG), were evaluated for the potential to identify and enumerate
specific bacterial groups in situ...
Marine bacterioplankton play an important role in global elemental cycles because they return carbon dioxide and nutrients to the biosphere as they reduce organic matter. Furthermore, marine bacterioplankton are not uniformly active, and subpopulations of the in situ community may be more or less active at any given time. Defining...
Batch cultures of Candidatus Pelagibacter ubique were grown under iron-, organosulfur-, and nitrogen-limiting conditions to understand how this ubiquitous marine bacterium responds to and interacts with environments where growth is limited by the availability of these nutrients. Global gene expression was monitored using microarrays and quantitative mass spectrometry to observe...
Different strains of Vibrio parahaemolyticus (Vp) in broth cultures and Vp-inoculated live Pacific oysters (Crassostrea gigas) were subjected to high pressure processing (HPP) at 241, 276, 310, and 345 MPa. Results showed Vp numbers were reduced by HPP in both pure culture and whole oysters. Vp inactivation was dependent on...
Microorganisms play key roles in ocean biogeochemistry. However, several
predominant groups of uncultured bacterioplankton thought to contribute to
important biogeochemical processes in the oceans are known primarily from gene
cloning studies. Although these studies have greatly expanded our view of
microbial diversity in the oceans, they are not quantitative and...
A new high-throughput culturing (HTC) method using a low nutrient
heterotrophic medium (LNHM) has led to the isolation of many novel strains of
oligotrophic bacteria from marine ecosystems. Four strains belonging to a single
dade, HTCC2151, HTCC218OT, HTCC2178T and HTCC2188T, were isolated
from the coast of Oregon by the HTC...
The phylogenetic diversity of two continental shelf picoplankton
communities was examined by analyzing SSU (16S) ribosomal RNA (rRNA)
genes amplified from environmental DNA with bacterial-specific primers and
the polymerase chain reaction (PCR). Picoplankton populations collected from
the pycnocline (10 m) over the eastern continental shelf of the United States
near...
Symbiotic relationships of bacteria with higher organisms are
commonly observed in nature; however, the functional role of these
relationships is only rarely understood. This is particularly evident in
epibiotic bacterial associations in the marine environment where the bacteria
are often a diverse ensemble of microorganisms, thus complicating the
identification of...
The objective of this project was to use ribosomal RNA genes, cloned
from natural populations of Sargasso Sea bacterioplankton, as markers for
picoplankton diversity. It is widely recognised that a majority of
microorganisms have yet to be cultivated, and therefore much of extant
microbial diversity remains unknown (50). The method...
Biological di-nitrogen (N₂) fixation is a key process in open-ocean ecosystems, where the new nitrogen (N) provided by marine diazotrophs can support a large fraction of primary productivity and carbon (C) drawdown. Recent laboratory studies have shown that elevated pCO₂ enhances the rate of N₂ fixation by select laboratory isolates...
Members of the SAR11 clade of heterotrophic α-proteobacteria are ubiquitous and abundant in the world's oceans where they are thought to play a pivotal role in the global carbon cycle. The first SAR11 bacterium cultivated in vitro, 'Candidatus Pelagibacter ubique' HTCC1062 (Ca. P. ubique), was isolated by dilution into sterile...
The starvation-survival patterns of 16 freshly isolated open
ocean bacteria and in a psychrophilic Vibrio sp., Ant-300, were
determined. These isolates displayed three survival patterns as
determined by viable cell count. These were (a) a rapid increase
followed by a decrease to a constant value (pattern of Ant-300 and
7...
The physiological responses of populations of a marine
Pseudomonas sp. to nutrient starvation were observed for a period
of 40 days. During the first 25 days of starvation the viability
of the population decreased by 99.9 percent, but thereafter the
cultures maintained approximately 5 x 10⁵ viable cells per ml...
The transport response of four marine psychrophilic bacteria
to a variety of substrates was determined and related to environmental
conditions. Studies on pressure and temperature effects on glutamic
acid transport and utilization indicated that high pressures and
low temperatures inhibit glutamate transport, while permitting glutamate
respiration. Similar results were obtained...
SAR11 Alphaproteobacteria are the most abundant aerobic chemoheterotrophs in ocean surface waters. Previous studies have indicated SAR11 cells play an important role in marine carbon cycling and consume up to half of some common dissolved organic compounds, such as amino acids. During sequencing of the first SAR11 genome, genes for...
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2. One Carbon Metabolism in SAR11 Pelagic MarineBacteria
Vibrio marinus, strain MP-1, was shown to grow from pH 6.7
to 8.5, with an optimum at 7.3. Growth was inhibited below salinity
10%₀ and above 60%₀ . The upper temperature limit of
growth was 20 C, and growth was very rapid with aeration at 15 C.
Heating of the...
Over 100 monthly bacterioplankton DNA samples, from each of the surface and 200 m depths at the Bermuda Atlantic Time-series Study (BATS) site, were analyzed for community assembly processes. Correlation networks, filtered for potential autocorrelation artifacts, were constructed for each depth. Network characteristics for the two depths were remarkably similar...
Historically, the difficulty of obtaining pure cultures of abundant marine
microbial plankton has an obstacle to reconstructing the underlying
mechanisms of biogeochemistry in the ocean. While a number of dominant
marine species from the ocean surface have been cultured, the dominant
microbial plankton of the dark ocean proved far more...
Marine bacteria play vital roles in every niche of the ocean, from small-scale symbioses to large-scale productivity and the regulation of Earth’s climate. Recent advances in molecular tools now allow us to probe the genetic potential of entire microbial communities. The next step is linking these diverse communities to the...
Oceanic carbon cycling plays a major role in determining global atmospheric CO₂. A better understanding of dissolved organic matter and its constituents in the water column and how it affects marine carbon cycling is sought after. This study successfully measured osmolytes, low molecular zwitterionic compounds derived from amino acids, in...