![[Feedback]](/icons/banner/feedbackACT.gif){kind=icon}
![[For Subscribers]](/icons/banner/subscriberACT.gif){kind=icon}
![[Archive]](/icons/banner/archiveACT.gif){kind=icon}
![[Search]](/icons/banner/searchACT.gif){kind=icon}
![[Contents]](/icons/banner/tocACT.gif){kind=icon}
Max Planck Institute for Marine Microbiology, Bremen, Germany
SUMMARY INTRODUCTION Units of Interest: Single Microbial Populations Marine Autotrophic Picoplankton as a Model Microbial Phenotypes Operational Phylogeny-Based Definition of Microbial Populations Synoptic Discussion of Marine and Freshwater Assemblages TOOLS, TECHNIQUES, AND STUDY CONCEPTS 16S rRNA Gene Clone Libraries: Essential but Prone to Bias Single-Cell Identification Problems with FISH and Possible Solutions Quantification of Abundance and Biomass Single-Cell Activities of Individual Populations Microautoradiography. Fluorescent activity tracers and flow sorting Distribution and Dynamics of Different Populations Experimental Enrichments in the Field Defined Laboratory Communities and Pure Culture Studies OCCURRENCE OF MICROBIAL POPULATIONS IN PLANKTON A Few Words on Diversity Bacterial Populations in the Marine Water Column Marine Archaea Numerically Important Bacteria in Freshwater Bacterial Populations Attached to Organic Particles FACTORS CONTROLLING MICROBIAL POPULATION SIZES Competition for Different Substrates Patchiness and Gradients Mortality Viral lysis. Selective predation. OUTLOOK ACKNOWLEDGMENTS REFERENCES
| SUMMARY |
|---|
 Top NextReferences |
|---|
| INTRODUCTION |
|---|
|
TopPreviousNextReferences |
|---|
A major goal of aquatic microbial ecology is to understand the specific roles of different microorganisms as mediators of element fluxes, e.g., during the remineralization of nutrients and organic carbon. So far, the novel molecular approaches have focused mainly on the occurrence and evolutionary relatedness of different bacteria, archaea, and picoeukaryotes. Clearly, there is a need to progress beyond a mere descriptive analysis of microbial diversity and community structure, to provide information about which microbes are involved in various biogeochemical processes. An integration of the more diversity-centered and the more biogeochemical perspectives in microbial ecology has been sought in the concept of the "structure and function" of microbial assemblages (73, 256). Such terminology might be fully appropriate for the study of technologically designed environments that serve particular functions, e.g., wastewater treatment plants, of coherent physiological groups, or of habitats like sediments or biofilms that feature a rigid physical structure (37, 257, 308). However, the concept of "structure and function" appears to overemphasize the "bottom-up" aspect of aquatic microbial assemblages, i.e., aspects that are related to microbial substrate and nutrient utilization. Pelagic habitats are also zones of high microbial mortality, and a substantial fraction of bacterial biomass may be transferred to higher trophic levels by predation (272). In order to understand the different heterotrophic microbes that inhabit the marine and freshwater plankton, it might thus be more adaeqate to consider both the specific "role" and the "fate" of microbial populations.
In many respects "aquatic microbial communities" are theoretical concepts rather than biologically real entities with (physical) structure, common genome or evolutionary history (66). Although ultimately there might be community assemblage rules also for the aquatic microbes (118), bacterioplankton assemblages could likewise be regarded as more or less loose collections of individual genotypic populations that change over time in features such as growth, mortality, and size. Here we discuss the advantages of adapting such a "Gleasonian" viewpoint (87), i.e., we focus on distinct bacterial populations that can be reliably identified and quantified in aquatic assemblages rather than on microbial community structure, diversity, or function as a whole. Specifically, we review current methodological approaches, and we assemble information about the occurrence, the phenotypic properties, and the possible role and fate of such defined microbial populations in the water column.
The diversity of phenotypes within aquatic microbes reflects the complexity of the habitats at a microscale (3, 106, 206, 281). For example, a large fraction of cells in coastal bacterioplankton may be motile during particular seasons or times of the day, and the duration of their actual swimming periods may be affected by substrate availability and patchiness (103). This might be related to chemosensory functions that allow bacteria to actively accumulate in substrate-rich microniches such as the phycosphere of senescent algae (15, 23). The balance between particle colonization efficiencies and detachment dynamics may even reflect species-specific microbial life cycles (100, 140, 141). Culturable genera of aquatic bacteria harbor large numbers of facultative anaerobes, and ten percent of bacteria in oxic coastal marine waters could incorporate glucose both at oxic and at anoxic conditions (4, 243). Some strains isolated from the plankton are capable of degrading complex organic molecules or of utilizing organic sulfur compounds (94, 95). Other aquatic bacteria differ in the duration of the lag phase that precedes growth in batch culture (212), exhibit high tolerance to UV radiation (290), secrete or resist antibiotics (61, 161), or are capable of cell communication by quorum sensing (97). In addition, indications of microbial activity are found in the water column that presently cannot be assigned to particular bacterial groups, e.g., microbial exoenzymes with contrasting kinetic properties (9, 307).
Aquatic microbes have moreover developed a range of specific defense strategies. Some freshwater bacteria form threadlike morphotypes or microcolonies that secrete large amounts of exopolymerous substances, thereby obtaining protection against ingestion by bacterivorous protists (113, 223). In coastal North Sea surface waters >25% of prokaryotes were covered by a polysaccharidic capsule, a feature of many pathogenic species (288) which again might be related to grazing resistance. A high percentage of bacteria in different freshwaters are gram-positive (263), which enhances their protection against digestion by unicellular eukaryotes (114, 125).
However, one must not conceptually merge distinct microbial species into fictional chimeric "aquatic bacteria" (Fig. 1). More appropriately, the various phenotypic features should be regarded as individual elements of unique life strategies that explain the occurrence and distribution patterns of different genotypes in aquatic habitats. Some of these phenotypic features, such as motility or filament formation, may be widespread across very different phylogenetic lineages (115), whereas others, e.g., antibiotic production or resistance, may be highly characteristic for particular species or genera (100, 160). A single genotype may express a variety of phenotypic features or even phenotypic plasticity (90, 115), and identical features may be shared by numerous genotypes. Thus, a central task of microbial ecology is to assign the various physiological abilities and phenotypes observed in situ to particular microbial species or genotypes.
|
|
The distinction of genotypic compartments within mixed microbial assemblages helps to compile ecologically relevant information about the abundances and activities of phylogenetically closely related groups of microorganisms, e.g., about their horizontal or vertical distribution patterns (210, 295), seasonality (63, 136), occurrence on particles (261), cell morphology (223), growth response to confinement (61, 72, 254), sensitivity to predation (16), incorporation of particular substrates (47, 169, 306), or growth under anoxic conditions (4). Our conceptual framework thus encompasses investigations of the seasonal occurrence of pathogenic Vibrio spp. in coastal waters (83, 117), of the response of a specific clade of freshwater betaproteobacteria to food web manipulations (278), but also of the differences in the vertical distribution of Bacteria and Archaea in the open ocean (136). On the other hand, it may also refer to the relative contributions of genotypic populations to a single biogeochemical process, e.g., the roles of planktonic members of the Roseobacter or SAR11 lineage in sulfur cycling (96, 169, 170, 306, 323).
It should be noted that a microbial population that is defined above the level of the single clone might represent an operational rather than a natural category. Therefore, such an operational taxonomic unit will be limited in its usefulness to a particular study context, and it should be refined or expanded if found inadequate for a specific purpose (Fig. 2). Some phylogenetic clades might harbor organisms with closely related or even identical 16S rRNA gene sequences but rather different ecophysiological properties (128). Sometimes it may be useful to merge such strains into larger categories, e.g., to study the occurrence of genera associated with particular phytoplankton blooms (96, 323). At other instances it might be necessary to distinguish between closely related strains, e.g., to understand the ecological significance of physiological variability (27, 109, 128) (Fig. 2).
Can identical ecological concepts be meaningfully applied to communities composed of bacterial groups from completely different phylogenetic lineages? Our review may in parts substantiate such doubts, e.g., with respect to the role of allochthonous (156) or filament-forming (130) microorganisms in the two habitat types. Yet at the same time we illustrate that a focus on individual microbial populations also provides a platform to compare the ecological value of particular phenotypic traits, e.g., of motility and small cell size (103, 221, 238), or of specific growth strategies (65, 68, 212) in very different genotypes and assemblages across aquatic habitats.
The scope of this review is limited in several dimensions. We do not attempt to draw an exhaustive picture of the microbial ecology of heterotrophic aquatic microbes. Instead we try to integrate a rather diverse range of facets, focusing on current methodological and experimental approaches, and on empirical findings related to traditional topics of population ecology. We argue that during the last decade the study of aquatic microbial populations has developed into a rewarding field of research that is based on mature methodology. Since our focus lies on the ecology of different populations rather than on the study of total assemblages, we only marginally touch the rich literature on genetic fingerprinting or on the diversity of aquatic communities. We limit our discussion to the "ordinary saprophytes", i.e., to the predominantly chemoorganoheterotrophic microbes (although admittedly the borders between purely heteroorganotrophic and photoautotrophic energy acquisition by pelagic microbes do become more and more fuzzy [20, 327]). We ignore microbial assemblages in sediments, biofilms, or in engineered systems, and we do not discuss in detail the physicochemical environments of aquatic microbes, but rather point to more specialized reviews, e.g., about macroscopic organic aggregates or exopolymerous substances (206, 281).
| TOOLS, TECHNIQUES, AND STUDY CONCEPTS |
|---|
|
TopPreviousNextReferences |
|---|
| 16S rRNA Gene Clone Libraries: Essential but Prone to Bias |
|---|
|
TopPreviousNextReferences |
|---|
The diversity of sequences in PCR-generated clone libraries may often not quantitatively reflect the diversity of the sequence types that are present in the original sample (242, 294). Already the DNA extraction may introduce biases, e.g., against bacteria with gram-positive cell walls (69). Primers that are designed to target the majority of known bacterial 16S rRNA gene sequences may exhibit mismatches to unknown sequence types (45, 287), and the presence of particular sequence types in mixed DNA may influence the PCR amplification efficiencies of other templates (292).
As a consequence some phylogenetic groups of aquatic microorganisms are overrepresented in clone libraries, whereas others are absent. For example, bacteria affiliated to the Cytophaga/Flexibacter/Flavobacterium group of the Bacteroidetes were rarely found in 16S rRNA gene clone libraries from coastal marine water samples, yet they may represent one third of all bacteria in such habitats (47, 63). In a library of coastal North Sea surface waters 80% of sequence types were related to the marine SAR86 clade, whereas this group formed <10% of microbial cells (63). In addition, PCR may result in chimeric sequences from two templates, and it may thus even produce artificial sequence diversity (124, 155). These biases may affect not only clone libraries, but also PCR-based methods for the genotypic fingerprinting of microbial assemblages (183, 193).
Sometimes it is desirable to limit the analysis of microbial diversity to a defined phylogenetic subset, e.g., to marine archaea or to freshwater actinobacteria (173, 309). This can be achieved by PCR with primers that are specific for the 16S rRNA genes of the group of interest (287). Such primers may cause an underestimation of the potential diversity within a particular phylogenetic group, e.g., some uncultured freshwater actinobacteria show one or more mismatches with the available sets of specific primers (309). Moreover, sequences generated with specific primers often cover only a part of the total 16S rRNA gene, typically less than 1,000 base pairs (55, 287). Partial sequence information negatively affects the accuracy of phylogenetic reconstruction (163), and it limits the range of potential signatures for subsequent in situ population studies by hybridization. Preferably, clone libraries of almost complete 16S rRNA gene sequences should be produced with general bacterial or archaeal primers, and they should then be screened for particular groups of interest (173, 184, 309).
The potential target groups for population studies are defined from sequence data by reconstruction of phylogenetic relationships. This analysis aims at placing the new environmental sequence types into different clades or clusters and to establish stable branching patterns. It forms the base for a phylogenetically meaningful definition of single populations and for the design of the corresponding oligonucleotide probes. A discussion of the reconstruction of microbial phylogenies from 16S rRNA gene sequences would go beyond the range of this review, and we draw the reader's attention to specific publications on this subject (163, 164).
| Single-Cell Identification |
|---|
|
TopPreviousNextReferences |
|---|
The FISH analysis can be carried out at two levels (Fig. 3). For one, investigators may draw upon the rapidly expanding set of available probes (162) (Table 1). Most frequently, probes have been applied that are targeted to higher taxonomic levels, i.e., to Bacteria, Archaea, Eucarya, subgroups of Proteobacteria, gram-negative sulfate-reducing bacteria, clades of ammonium-oxidizing bacteria, etc. In an earlier review on FISH, such an analysis was proposed as a first step of a larger "top-to-bottom" strategy (7).
|
|
The second level of FISH analysis is more technically demanding. It includes the design and optimization of new FISH probes for individual phylogenetic clades or single phylotypes based on sequence information from 16S rRNA gene clone libraries of environmental DNA (Fig. 3). This strategy has been termed the "full-cycle rRNA approach" by one of the authors (7). The procedure is comparable to the testing of a scientific hypothesis. Specifically, it is verified if a particular clade of sequence types obtained from environmental DNA after PCR amplification indeed harbors microbes that form a substantial fraction of the assemblage in the studied habitat. The lower limits for a reliable quantification of cell numbers by the FISH approach as set by counting effort and negative controls typically range around 0.1 to 2% of total counts (217). Consequently, researchers applying FISH may need to test a number of newly designed specific probes on field samples to discover microbial populations that are sufficiently abundant for subsequent quantitative population studies. This implicit risk of falsification of a working hypothesis represents a major conceptual difference between the full-cycle rRNA approach and other strategies that analyze microbial assemblages by molecular fingerprinting of PCR-amplified rRNA genes (185, 254).
| Problems with FISH and Possible Solutions |
|---|
|
TopPreviousNextReferences |
|---|
However, the replacement of some of the first generation of available FISH probes should be seen as a necessary optimization process in a rapidly progressing field rather than as an irresolvable problem of the FISH approach. Analyses of rRNA gene sequences from aquatic habitats indicate that only a limited number of well-defined phylogenetic clades of microorganisms might actually be common in the pelagic zones of marine and freshwater environments (55, 85, 91, 121, 240, 328). A substantial amount of diversity within several of these clades appears to be covered adequately by the presently available sequence data (108). Such knowledge will eventually provide a reliable base for a new generation of more "habitat-specific" FISH probes that discriminate well-established lineages of microbes in a particular environment (Table 1), e.g., the various marine SAR clades (62, 188, 189, 325) or the freshwater actinobacteria (91, 310).
Another drawback of FISH with fluorescently monolabeled oligonucleotide probes is the low fluorescence intensity of hybridized bacteria from natural water samples (214). Bacteria in oligotrophic water are often small, slow growing, or in stationary phase (187), and their ribosome content is typically low (65). Consequently, there are few rRNA target molecules for FISH staining. The fraction of microbial cells that can be visualized microscopically may thus vary with the physiological state of the studied assemblage. For example, a significantly smaller percentage of bacteria could be stained by FISH in coastal North Sea surface waters during the winter months than during the spring and summer seasons (63). In environments such as offshore marine waters, sometimes only a minor fraction of microbes can be visualized by FISH with fluorescently monolabeled oligonucleotide probes (214). Therefore, it is likely that the abundances of some slowly-growing microorganisms with small cell sizes, e.g., of members of the marine SAR86 clade, are underestimated by the standard FISH approach (210).
During the last decade, efforts have been made to increase the sensitivity of FISH, e.g., with peptide nucleic acid probes (320), brighter fluorochromes (88), image intensified video microscopy (78), preincubation with chloramphenicol (200), hybridization with more than one fluorescently labeled oligonucleotide probe (188), and helper probes (70). Two particularly promising alternative strategies to FISH with fluorescently monolabeled oligonucleotides are polynucleotide probes and enzymatic signal amplification (57, 149, 210). Fluorescently multilabeled rRNA-targeted polyribonucleotide probes yield significantly higher signal intensities than oligonucleotide probes (214). They have been successfully applied to discriminate between bacteria and different groups of archaea in coastal and open ocean environments (40, 136, 214). Limitations of polyribonucleotide probes as a routine tool for the identification of aquatic microbes are the relatively high effort and variability of enzymatic probe synthesis, and the rather low phylogenetic resolution. Only three large taxa have been distinguished by this technique in marine waters (57), although potentially a resolution at the genus level is possible (300).
A working alternative is catalyzed reporter deposition (CARD)-FISH (210, 211, 263), which combines in situ hybridization with horseradish peroxidase labeled oligonucleotide probes and enzymatic signal amplification with fluorescently labeled tyramides (24). This allows the quantitative detection of marine and freshwater pelagic bacteria with low ribosome content that are insufficiently visualized by fluorescently monolabeled probes (210, 263) (Fig. 4).
|
| Quantification of Abundance and Biomass |
|---|
|
TopPreviousNextReferences |
|---|
A conversion of cell numbers into biomass is required for the reconstruction of carbon fluxes through microbial food webs. Bacterial cell sizes and the relationship between cell size and dry mass can be determined empirically, e.g., by image analyzed microscopy (174, 274) and appropriate conversion factors (159, 197, 233). Some microbial taxa in the plankton form significantly larger cells than others (16), and population changes within such groups may thus contribute disproportionally to changes in total biomass (132, 222). The most extreme example are the filamentous bacteria in the water column of many lakes (130). Such morphotypes rarely form more than a few percent of total cell numbers, but they may temporarily constitute half of total microbial biomass or more (130, 286) (Fig. 5). Therefore, the biomasses of different microbial populations may need to be determined separately in order to assess their respective roles in the carbon flux through aquatic systems (46, 132, 216, 237).
|
| Single-Cell Activities of Individual Populations |
|---|
|
TopPreviousNextReferences |
|---|
With the exception of stable isotope analysis (236) or pulse-labeling of nucleic acids (302), physiological information is typically lost by methods that use DNA or rRNA extracts for microbial identification. By contrast, physiological properties can be readily related to a particular genotype at the single cell level. FISH by itself may already provide some information about the physiological state of a population, because the signal intensity of hybridization is proportional to cellular ribosome content. The ribosome content of marine isolates tends to increase with growth rate (138). However, rRNA concentration is a parameter that may sometimes be difficult to interpret. Some marine bacteria may maintain high numbers of ribosomes even during periods of prolonged starvation (68). This is probably essential to rapidly respond to changes in growth conditions in a patchy environment (212). Thus, ribosome content may allow a limited assessment of bacterioplankton "activity" at the community level (52, 80), but it needs to be interpreted with caution if single populations are to be compared. In addition, cell identification by FISH can be combined with a number of other methods that visualize particular physiological properties of individual cells, e.g., substrate uptake, DNA synthesis, respiration (47, 196, 213), and even with stable isotope probing (198).
Microautoradiography. One of the most powerful approaches to study physiological activities in mixed microbial assemblages dates back to the 1960s. The uptake of radiolabeled tracer substrates into individual cells can be visualized by a photographic technique termed microautoradiography (30, 31) (Fig. 6a). In combination with cell identification by FISH, this approach allows us to assess the partitioning of substrate consumption between different microbial populations in mixed assemblages. Microautoradiography-FISH was first used to determine organic and inorganic substrate uptake of ammonia-oxidizing bacteria and of other groups in activated sludge (154), but has since then been adapted for microbes in lakes and in the marine water column (4, 47, 98, 169, 199, 296, 306). Recently, protocols have been developed that integrate the superior CARD-FISH staining with microautoradiography for the analysis of bacterial substrate uptake in environments such as the mesopelagic zone (4, 296). It has even been attempted to add a quantitative aspect to microautoradiography by estimating the amount of incorporated radiolabel from the number of grains that are formed around active cells (46, 168, 170).
|
Fluorescent activity tracers and flow sorting In order to study particular aspects of growth in individual microbial populations there are technically less demanding alternatives to microautoradiography. Pelagic bacteria with an active electron transport system of the respiratory chain reduce tetrazolium salts to water-insoluble crystals (322). Such formazan grains are deposited intracellularly, and they can be detected both microscopically (247) and by flow cytometry (54). In combination with FISH cell respiration can thus be visualized in single microbial populations, as was shown for filamentous bacteria from activated sludge (196). However, the tetrazolium reduction method appears to be a rather insensitive means to distinguish between growing and non-growing (or dead) bacteria in the plankton. Accordingly, bacteria with visible formazan deposits are regarded as the most highly active fraction within a larger set of growing cells (268). While there may be good reasons to identify such highly active bacterial populations, no investigation has combined tetrazolium reduction and FISH to study microbes in the water column of natural aquatic systems.
Bromodeoxyuridine is a halogenated nucleotide analogue of thymidine that is incorporated into newly synthesized DNA of bacteria and eukaryotes (213, 245, 302). It provides a non-radioactive alternative to microautoradiography with tritiated thymidine (207) and it allows us to quantify growth rates at the single-cell level (116). Bromodeoxyuridine incorporation has been combined with CARD-FISH to visualize de novo DNA synthesis in different freshwater and marine bacterial populations (209, 213, 310) (Fig. 6b). This offers a sensitive means to detect changes of growth rates in single microbial populations in situ. During bottle incubations of filtered seawater, a rise in the numbers of bromodeoxyuridine incorporating Alteromonas sp. cells clearly preceded cell multiplication (213). Significant seasonal differences and short-term variability of growth rates were observed in members of the Roseobacter spp. and NOR5 lineages from coastal North Sea picoplankton (209). High bromodeoxyuridine incorporation by actinobacteria in mountain lakes indicated that these bacteria were not passively introduced from soils, but autochthonously growing members of the bacterioplankton community (310).
Flow cytometry may provide an alternative means of detecting activity or substrate uptake in single microbial cells. It allows the physical sorting of particular bacterial populations of interest for further analyses (22, 72). So far, microbial cells from plankton samples have been mainly sorted by phenotypic features, e.g., cell volume or cellular DNA or protein content (72, 150, 267, 326). Sorted bacteria have been analyzed by molecular methods (21, 323) and for radiotracer incorporation (151, 327). In contrast to microautoradiography, the tracer uptake rates of specific cell populations can be readily quantified by this approach.
Direct sorting of microbial cells after FISH staining has first been shown in highly productive wastewater treatment systems (284). Recently this approach has also been adapted for bacterial cells from coastal marine bacterioplankton, taking advantage of the superior signal intensities of CARD-FISH staining (262). Such a combination of cell identification and flow sorting potentially offers the ability to quantitatively investigate substrate uptake of single populations in natural samples (327). Moreover, it might eventually provide a means of obtaining functional genes or larger genome fragments from phylogenetically coherent groups of microbes directly sorted from environmental samples.
For the purpose of gaining ecological insight from spatial or temporal distribution patterns, binary information about the presence or absence of a particular bacterial group, as provided by cloning or fingerprinting techniques, is probably insufficient. Such approaches allow us to detect fundamental differences between communities, e.g., between marine and freshwater habitats (180), along rivers (264), or in mesocosm (244, 253), but they can hardly distinguish if a set of environmental variables is more or less favorable for a specific population. A too-coarse division of aquatic microbial assemblages, e.g., into subphyla of Proteobacteria by FISH with the respective probes (171), also suffers from drawbacks, since different populations with potentially contrasting dynamics might be put into ecologically meaningless categories (Fig. 2). Such studies may contribute to our understanding of large biogeographic divisions, e.g., between marine and freshwater habitats (89), and of basic discontinuities in the composition of microbial assemblages, e.g., along estuaries (28). However, both the qualitative community analyses by fingerprinting and investigations on large taxonomic units by FISH should be regarded as intermediate steps towards the quantitative study of ecologically coherent and phylogenetically more tightly-defined populations.
Such investigations are often plagued by the mysterious "bottle effect," a hard-to-define concept that reflects the worry of whether phenomena observed in confined assemblages are nonspecific consequences of the confinement rather than a result of the planned manipulation. Nevertheless, experimental mesocosms are among the few tools available to microbial ecologists that go beyond a purely descriptive analysis of aquatic microbial assemblages. A number of well-defined hypotheses about microbial populations have been successfully addressed by such approaches (16, 61, 132, 223, 244, 278, 293).
Thus, laboratory investigations on bacterial isolates or model communities add another important dimension to the understanding of microbial population ecology. For example, particular physical structures within aquatic habitats cannot be preserved in experimental approaches in the field. Laboratory systems can artificially produce aggregated organic matter in natural water samples (101) and trap single flocs in a three-dimensional flux field (230). Such designs provide the adequate physical and chemical environment to study microbial activities and successions on organic aggregates and particles (100-102).
Laboratory studies may also provide a better control over parameters that might mask the hypothesized relationship between the studied population and the variable of interest. Continuous-cultivation systems, not necessarily chemostats (126), stabilize the composition of mixed assemblages by enforcing a minimal growth rate and by providing constant temperature, illumination, and input of substrates and nutrients. This allows us to experimentally sustain transient ecological phenomena over prolonged periods of time, e.g., the rise of particular predator populations (112, 221, 232, 234, 250, 279), bacterial-viral interactions (181), or the breakdown of cyanobacterial blooms (304).
Investigations on pure cultures offer the possibility to distinguish between phenotypic and physiological properties of different aquatic bacteria, e.g., in their interactions with algae (29, 99, 146), their chemotactic responses (15, 23), motility patterns (140), grazing sensitivity (27, 114), or cell filamentation (115, 273). This provides the opportunity to test hypotheses about the ecological relevance of such features.
| OCCURRENCE OF MICROBIAL POPULATIONS IN PLANKTON |
|---|
|
TopPreviousNextReferences |
|---|
Evidence has accumulated that there is relatively little overlap between the phylogenetic groups that are present in marine and freshwater environments (89, 180, 241), e.g., specific groups of archaea appear to be entirely limited to the marine water column (59, 76, 173). Lineages of 16 rRNA gene sequence types that occur in both habitat types include the SAR11 clade of Alphaproteobacteria (14, 85, 329), and the ammonia-oxidizing Betaproteobacteria (123, 297). Even within these clades, distinct clusters of marine and freshwater sequence types can be distinguished (329). Some clades of actinobacteria typically found in freshwater habitats also contain sequences from estuaries and marine waters (48, 309), whereas other clades within this phylum are exclusively of either marine or freshwater origin (91, 240, 309, 328). Members of the very diverse Cytophaga/Flexibacter/Flavobacterium group are common in some coastal and offshore marine habitats (45, 63, 144, 280), but they also occur in rivers and lakes (28, 143, 218, 223). Bacteria from this group appear to have radiated across a range of aquatic habitats, including biofilms and sediments (34, 158).
The phylogenetic ties between freshwater and soil microbes are still unclear. Sequence types from both environments have, e.g., been found within the freshwater acIV lineage of the actinobacteria (309). There are furthermore indications that microbial assemblages in some lakes may be similar to those in the influx from the catchment (156).
In the context of this review we distinguish between the multitude of microbial phylogenetic lineages that may occur in various aquatic systems and the few groups of microbes that have been shown to form substantial populations in such environments. Clearly, archival listings of microbial diversity from different habitats are a crucial first step to investigate the role and fate of aquatic microbes, since they provide the essential fundament for subsequent studies about the ecology of particular populations. However, it is equally important to progress from a purely qualitative appreciation of microbial diversity to the quantification of the abundances, biomasses, and activities of different phylogenetic groups. For example, it is presently still unclear if members of the Verrucomicrobia are an important component of freshwater assemblages. Such bacteria are frequently detected in lakes by PCR-based methods (157, 330, 331). From all we know, their densities might be one in a million but potentially also >10% of all cells. The following sections thus specifically discuss investigations that have established the cell concentrations, spatial distributions, temporal successions, or physiological features of specific microbial taxa in the plankton of marine and freshwater systems.
|
The composition of microbial communities in more extreme habitats might sometimes be very simple. Hydrothermal circulation activities in deep sea environments produce buoyant plumes with substantially elevated levels of reduced chemicals. The bacterial assemblages within such a plume inside the caldera of the Suiyo Seamount volcano consisted almost entirely of two distinct phylogenetic populations that were related to sulfur-oxidizing symbionts of hydrothermal vent fauna (291). The caldera might thus represent a giant natural continuous-cultivation system for these two groups.
Sometimes, it may be necessary to define microbial populations at the level of single strains, e.g., for the study of pathogenic Vibrio spp. in marine waters. In coastal environments Vibrio cholerae can be found both attached on particles and free-living in the water column (44), and pronounced seasonal and horizontal differences in population sizes have been reported (83, 117). In microcosms spiked with V. cholerae, rapid growth of these bacteria was observed after addition of organic carbon (190). It is thus conceivable that anthropogenic eutrophication might indirectly favor the growth and dispersal of pathogenic Vibrio strains.
The metabolic capacities of planktonic crenarchaea are unclear, but there are indications that members of this lineage might be auto- or mixotrophic (120, 321). The planktonic marine Euryarchaeota on the other hand appear to be a common element of coastal assemblages and surface waters. Members of this lineage seasonally formed >30% of all cells in the surface picoplankton of the North Sea (214) (Fig. 7). Seasonal blooms of Euryarchaeota were also observed during a long-term study in surface waters of the upper Santa Barbara Channel (191).
In contrast to the lake snow assemblages, riverine organic particles have been described to mainly harbor Betaproteobacteria related to the drinking water biofilm bacterium Aquabacterium commune. These bacteria formed up to 30% of all cells on lotic organic aggregates in the river Elbe (135). The composition of the microbial assemblages on such aggregates showed pronounced seasonal changes, and bacteria related to the Planctomycetales were absent in winter.
| FACTORS CONTROLLING MICROBIAL POPULATION SIZES |
|---|
|
Top |
|---|
