David L. Kirchman

Microbial ecology of the oceans

Marine microbes - an overview evolution, diversity and molecular ecology of marine Prokaryotes bacterial production and biomass in the oceans production mechanisms of dissolved organic matter heterotrophic bacteria and the dynamics of dissolved organic material UV radiation effects on microbes and microbial processes control of bacterial growth in idealized food webs. (Part contents)

The ecology of Cytophaga–Flavobacteria in aquatic environments

Culture-dependent and -independent studies have found that prokaryotic assemblages are quite diverse in aquatic habitats and contain representatives of virtually all of the roughly 40 divisions of bacteria and the major archaeal groups found so far in the biosphere [1]. Fortunately, not all of these prokaryotic groups are abundant in the plankton nor important in all biogeochemical cycles. Autotrophic and heterotrophic bacteria dominate the prokaryotic biomass in surface waters, as Archaea appear to be abundant only in the plankton of the deep oceans [2]. Among the heterotrophic bacteria, the two most abundant groups are often the Proteobacteria and the subject of this review, the Cytophaga–Flavobacteria cluster (Table 1). View this table: 1 The relative abundance of the major heterotrophic bacterial groups in aquatic ecosystems, as determined by FISH with oligonucleotide probes This paper reviews recent studies that have applied molecular methods to examine uncultured Cytophaga–Flavobacteria in freshwaters and the oceans, with the ultimate goal of using this information to better understand the role of heterotrophic bacteria in carbon cycles and other biogeochemical processes. The importance of heterotrophic bacteria in biogeochemical processes is now well appreciated, but until recently geochemists and field-orientated microbial ecologists considered these microbes as if they were a single group, even though microbiologists have been accumulating for several years information about the taxonomic and phylogenetic make up (‘community structure’) of heterotrophic bacterial communities. Only recently, however, have microbial ecologists been able to link community structure with specific biogeochemical processes (‘function’) [3]. Here I summarize briefly our progress in these areas while discussing what we know about Cytophaga–Flavobacteria in aquatic habitats. This microbial group is a natural starting point because of its high abundance in many freshwater and marine systems. The Cytophaga–Flavobacteria cluster belongs to a diverse bacterial division that has been labeled differently over …

Natural Assemblages of Marine Proteobacteria and Members of the Cytophaga-Flavobacter Cluster Consuming Low- and High-Molecular-Weight Dissolved Organic Matter

ABSTRACT We used a method that combines microautoradiography with hybridization of fluorescent rRNA-targeted oligonucleotide probes to whole cells (MICRO-FISH) to test the hypothesis that the relative contributions of various phylogenetic groups to the utilization of dissolved organic matter (DOM) depend solely on their relative abundance in the bacterial community. We found that utilization of even simple low-molecular-weight DOM components by bacteria differed across the major phylogenetic groups and often did not correlate with the relative abundance of these bacterial groups in estuarine and coastal environments. The Cytophaga-Flavobacter cluster was overrepresented in the portion of the assemblage consuming chitin,N-acetylglucosamine, and protein but was generally underrepresented in the assemblage consuming amino acids. The amino acid-consuming assemblage was usually dominated by the α subclass of the class Proteobacteria, although the representation of α-proteobacteria in the protein-consuming assemblages was about that expected from their relative abundance in the entire bacterial community. In our experiments, no phylogenetic group dominated the consumption of all DOM, suggesting that the participation of a diverse assemblage of bacteria is essential for the complete degradation of complex DOM in the oceans. These results also suggest that the role of aerobic heterotrophic bacteria in carbon cycling would be more accurately described by using three groups instead of the single bacterial compartment currently used in biogeochemical models.

Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean

The biological pump is a process whereby CO2 in the upper ocean is fixed by primary producers and transported to the deep ocean as sinking biogenic particles or as dissolved organic matter. The fate of most of this exported material is remineralization to CO2, which accumulates in deep waters until it is eventually ventilated again at the sea surface. However, a proportion of the fixed carbon is not mineralized but is instead stored for millennia as recalcitrant dissolved organic matter. The processes and mechanisms involved in the generation of this large carbon reservoir are poorly understood. Here, we propose the microbial carbon pump as a conceptual framework to address this important, multifaceted biogeochemical problem.

Community Composition of Marine Bacterioplankton Determined by 16S rRNA Gene Clone Libraries and Fluorescence In Situ Hybridization

ABSTRACT We determined the compositions of bacterioplankton communities in surface waters of coastal California using clone libraries of 16S rRNA genes and fluorescence in situ hybridization (FISH) in order to compare the community structures inferred from these two culture-independent approaches. The compositions of two clone libraries were quite similar to those of clone libraries of marine bacterioplankton examined by previous studies. Clones from γ-proteobacteria comprised ca. 28% of the libraries, while approximately 55% of the clones came from α-proteobacteria, which dominated the clone libraries. TheCytophaga-Flavobacter group and three others each comprised 10% or fewer of the clone libraries. The community composition determined by FISH differed substantially from the composition implied by the clone libraries. The Cytophaga-Flavobacter group dominated 8 of the 11 communities assayed by FISH, including the two communities assayed using clone libraries. On average only 10% of DAPI (4′,6′-diamidino-2-phenylindole)-stained bacteria were detected by FISH with a probe for α-proteobacteria, but 30% of DAPI-stained bacteria appeared to be in the Cytophaga-Flavobacter group as determined by FISH. α-Proteobacteria were greatly overrepresented in clone libraries compared to their relative abundance determined by FISH, while the Cytophaga-Flavobacter group was underrepresented in clone libraries. Our data show that theCytophaga-Flavobacter group can be a numerically dominant component of coastal marine bacterioplankton communities.

Ecology of the rare microbial biosphere of the Arctic Ocean

Understanding the role of microbes in the oceans has focused on taxa that occur in high abundance; yet most of the marine microbial diversity is largely determined by a long tail of low-abundance taxa. This rare biosphere may have a cosmopolitan distribution because of high dispersal and low loss rates, and possibly represents a source of phylotypes that become abundant when environmental conditions change. However, the true ecological role of rare marine microorganisms is still not known. Here, we use pyrosequencing to describe the structure and composition of the rare biosphere and to test whether it represents cosmopolitan taxa or whether, similar to abundant phylotypes, the rare community has a biogeography. Our examination of 740,353 16S rRNA gene sequences from 32 bacterial and archaeal communities from various locations of the Arctic Ocean showed that rare phylotypes did not have a cosmopolitan distribution but, rather, followed patterns similar to those of the most abundant members of the community and of the entire community. The abundance distributions of rare and abundant phylotypes were different, following a log-series and log-normal model, respectively, and the taxonomic composition of the rare biosphere was similar to the composition of the abundant phylotypes. We conclude that the rare biosphere has a biogeography and that its tremendous diversity is most likely subjected to ecological processes such as selection, speciation, and extinction.

The Uptake of Inorganic Nutrients by Heterotrophic Bacteria

It is now well known that heterotrophic bacteria account for a large portion of total uptake of both phosphate (60% median) and ammonium (30% median) in freshwaters and marine environments. Less clear are the factors controlling relative uptake by bacteria, and the consequences of this uptake on the plankton community and biogeochemical processes, e.g., new production. Some of the variation in reported inorganic nutrient uptake by bacteria is undoubtedly due to methodological problems, but even so, uptake would be expected to vary because of variation in several parameters, perhaps the most interesting being dissolved organic matter. Uptake of ammonium by bacteria is very low whereas uptake of dissolved free amino acids (DFAA) is high in eutrophic estuaries (the Delaware Bay and Chesapeake Bay). The concentrations and turnover of DFAA are insufficient, however, in oligotrophic oceans where bacteria turn to ammonium and nitrate, although the latter only as a last resort. I argue here that high uptake of dissolved organic carbon, which has been questioned, is necessary to balance the measured uptake of dissolved inorganic nitrogen (DIN) in seawater culture experiments. What is problematic is that this DIN uptake exceeds bacterial biomass production. One possibility is that bacteria excrete dissolved organic nitrogen (DON). A recent study offers some support for this hypothesis. Lysis by viruses would also release DON.While ammonium uptake by heterotrophic bacteria has been hypothesized to affect phytoplankton community structure, other impacts on the phytoplankton and biomass production (both total and new) are less clear and need further work. Also, even though bacteria account for a very large fraction of phosphate uptake, how this helps to structure the plankton community has not been examined. What is clear is that the interactions between bacterial and phytoplankton uptake of inorganic nutrients are more complicated than simple competition.

Activity of abundant and rare bacteria in a coastal ocean

The surface layer of the oceans and other aquatic environments contains many bacteria that range in activity, from dormant cells to those with high rates of metabolism. However, little experimental evidence exists about the activity of specific bacterial taxa, especially rare ones. Here we explore the relationship between abundance and activity by documenting changes in abundance over time and by examining the ratio of 16S rRNA to rRNA genes (rDNA) of individual bacterial taxa. The V1–V2 region of 16S rRNA and rDNA was analyzed by tag pyrosequencing in a 3-y study of surface waters off the Delaware coast. Over half of the bacterial taxa actively cycled between abundant and rare, whereas about 12% always remained rare and potentially inactive. There was a significant correlation between the relative abundance of 16S rRNA and the relative abundance of 16S rDNA for most individual taxa. However, 16S rRNA:rDNA ratios were significantly higher in about 20% of the taxa when they were rare than when abundant. Relationships between 16S rRNA and rDNA frequencies were confirmed for five taxa by quantitative PCR. Our findings suggest that though abundance follows activity in the majority of the taxa, a significant portion of the rare community is active, with growth rates that decrease as abundance increases.

Measuring bacterial biomass production and growth rates from leucine incorporation in natural aquatic environments

Publisher Summary An estimate of microbial production is used as a general index of microbial activity, and specifically, to calculate growth rates. Biomass production is used to obtain a first-order estimate of rates of several processes mediated by microbes. In the case of heterotrophic bacteria, biomass production is used to estimate use of dissolved organic material (DOM) if coupled with an estimate of the growth efficiency. DOM uptake equals bacterial biomass production divided by the growth efficiency (expressed as a fraction, not a percentage). Biomass production is the increase in biomass per unit time per unit volume or per area and is a function of both biomasses (B), usually expressed as carbon mass per volume—for example, μgC l-1—and the specific growth rate (μ) (e.g.h1). The methods used to examine bacterial production in aquatic environments are either thymidine (TdR) incorporation, or leucine (Leu) incorporation. Both are rapid, easy, and specific for heterotrophic bacteria. This leucine method is discussed, as it is more straightforward than the TdR method for estimating the bacterial production. Two variations of the Leu method are described; however, the basic biochemistry and physiology behind the methods are the same.

Microbial growth in the polar oceans — role of temperature and potential impact of climate change

Heterotrophic bacteria are the most abundant organisms on the planet and dominate oceanic biogeochemical cycles, including that of carbon. Their role in polar waters has been enigmatic, however, because of conflicting reports about how temperature and the supply of organic carbon control bacterial growth. In this Analysis article, we attempt to resolve this controversy by reviewing previous reports in light of new data on microbial processes in the western Arctic Ocean and by comparing polar waters with low-latitude oceans. Understanding the regulation of in situ microbial activity may help us understand the response of the Arctic Ocean and Antarctic coastal waters over the coming decades as they warm and ice coverage declines.