Viruses and the microbial loop

The abundance of viral-like particles in marine ecosystems ranges from <104 ml^–1 to >10⁸ ml^–1. Their distribution in time and space parallels that of other biological parameters such as bacterial abundance and chlorophyll a. There is a lack of consensus between methods used to assess viral activity, i.e., rate of change in viral abundance (increase or decrease). The highest rates, 10–100 days^–1, are observed in experiments with short sampling intervals (0.2–2 h), while lower rates, on the order of 1 day^–1, are observed in experiments with longer sampling intervals (days). Few studies have been carried out, but viruses appear, at least in some cases, to have a significant impact on carbon and nutrient flow in microbial food webs. Viruses have also been demonstrated to exert a species specific control of both bacteria and phytoplankton populations in natural waters.     

Incorporating the microbial loop in a simple plankton model

The microbial loop, which recycles nutrients in the upper layers of the ocean, is an integral part of plankton dynamics. The usual method for modelling the complex patterns involved has been to consider the ''Z'' in N/P/Z (nutrient/phytoplankton/zooplankton) models as containing all possible grazers on P and, implicitly, relegate the carnivorous metazoans to the loss term on Z. I propose the opposite approach (to define Z explicitly as the metazoans responsible for export fluxes) and to simulate the effects of the microbial loop implicitly in terms of grazing and excretion rates. The reasons for taking this alternative route are (i) the importance of copepods in the carbon/nitrogen flux from the euphotic zone to deeper water compared with (ii) the predominantly internal role of the microzooplankton in recycling nutrients; and (iii) the problems of sampling the microbial component, compared with sampling larger metazoans. Finally, there is the need to keep plankton models as simple as possible for later use in coupled physical/biological systems.     

Factors influencing Gonyostomum semen blooms in a small boreal reservoir lake

Blooms of the nuisance alga Gonyostomum semen occurred in Lake 979 (Experimental Lakes Area), a small brown-water lake, that was subjected to several years of an experimental flooding regime. During periods of flooding, blooms of G. semen developed when light decreased below 100molm^–2s^–1 and total phosphorous concentrations increased to >30gl^–1. Gonyostomum semen biomass was significantly correlated with total P and DOC concentrations. In addition, G. semen abundance increased at times when Daphnia rosea had rapidly declined to<10 animals l^–1. Daphnia egg ratios suggest that declines in Daphnia abundance were the result of shifts in mortality and not causally linked to changes in G. semen densities. The results observed in Lake 979 were supported by a laboratory experiment where the appearance of G. semen from Lake 979 sediment was stimulated by altering chemical and biological variables. The stimulation of G. semen blooms appears to be dependant on multiple variables rather than a single variable.     

Hydrology is reflected in the functioning and community composition of methanotrophs in the littoral wetland of a boreal lake

In lake ecosystems a major proportion of methane (CH(4) ) emissions originate from the littoral zone, which can have a great spatial variability in hydrology, soil quality and vegetation. Hitherto, spatial heterogeneity and the effects it has on functioning and diversity of methanotrophs in littoral wetlands have been poorly understood. A diagnostic microarray based on the particulate methane monooxygenase gene coupled with geostatistics was used to analyse spatial patterns of methanotrophs in the littoral wetland of a eutrophic boreal lake (Lake Kev?t?n, Eastern Finland). The wetland had a hydrology gradient with a mean water table varying from -8 to -25 cm. The wettest area, comprising the highest CH(4) oxidation, had the highest abundance and species richness of methanotrophs. A high water table favoured the occurrence of type Ib methanotrophs, whereas types Ia and II were found under all moisture conditions. Thus the spatial heterogeneity in functioning and diversity of methanotrophs in littoral wetlands is highly dependent on the water table, which in turn varies spatially in relation to the geomorphology of the wetland. We suggest that changes in water levels resulting from regulation of lakes and/or global change will affect the abundance, activity and diversity of methanotrophs, and consequently CH(4) emissions from such systems.     

Photomineralization in a boreal hydroelectric reservoir: a comparison with natural aquatic ecosystems

In order to evaluate the role of photochemistry in the carbon dioxide (CO₂) generation from a 10-year-old boreal reservoir, the photomineralization of dissolved organic matter (DOM) was assessed and compared to a boreal river as well as to boreal and temperate lakes during July and August, 2003. Sterile water samples were irradiated by sunlight over the whole photoperiod and subsequently analyzed for CO₂. Mean energy-normalized apparent photochemical yield of CO₂ (an index of DOM photoreactivity normalized for the energy absorbed by samples) was significantly higher in the reservoir (27.7 ± 13.0 mg CO₂·m⁻³·kJ⁻¹) and the boreal river (35.8 ± 2.3 mg CO₂·m⁻³·kJ⁻¹) than in the boreal lakes (15.5 ± 5.1 mg CO₂·m⁻³·kJ⁻¹). The DOM photoreactivity of the temperate lakes (20.9 ± 8.1 mg CO₂·m⁻³·kJ⁻¹) was not statistically different from any type of boreal water bodies. There was no significant difference in either the integrated photoproduction of CO₂ (273–433 mg CO₂·m⁻²·d⁻¹) or the potential photochemical contribution to CO₂ diffusive fluxes (56–92%) among these water bodies. DOM photoreactivity was significantly affected by the cumulative hydrological residence time (CHRT) when considering the whole data set. However, when considering only the boreal water bodies, iron (Fe) and manganese (Mn) also intervened. The fact that DOM photoreactivity was related to CHRT as well as to Fe and Mn concentrations, which are respectively permanent and long-lasting features of the reservoir, suggests that the photoproduction of CO₂ is not likely to decrease over time. This process may therefore play a substantial role in the long-term CO₂ emissions from boreal reservoirs during the summer, its potential contribution to CO₂ diffusive fluxes being estimated at 56 ± 29 %.     

Litre-scale microbial fuel cells operated in a complete loop

Using the anode effluent to compensate the alkalinization in a bio-cathode has recently been proposed as a way to operate a microbial fuel cell (MFC) in a continuous and pH neutral way. In this research, we successfully demonstrated that the operation of a MFC without any pH adjustments is possible by completing the liquid loop over cathode and anode. During the complete loop operation, a stable current production of 23.2 ± 2.5 A m⁻³ MFC was obtained, even in the presence of 3.2–5.2 mg O₂ L⁻¹ in the anode. The use of current collectors and subdivided electrical circuitries for relative large 2.5-L-scale MFCs resulted in ohmic cell resistances in the order of 1.4–1.7 mΩ m³ MFC, which were comparable to values of ten times smaller MFCs. Nevertheless, the bio-cathode activity still needs to be improved significantly with a factor 10–50 in order achieve desirable current densities of 1,000 A m⁻³ MFC. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The microbial loop in flowing waters

The microbial loop in flowing waters is dependent on allochthonous sources of carbon, which vary in quality. The proportion of dissolved organic carbon (DOC) that can be degraded ranges from <1 to over 50%, and the bioavailability of DOC (micrograms bacterial biomass produced per milligram DOC present) ranges over two orders of magnitude. Bioavailability of DOC is predictable from the ratio of H/C and O/C of the DOC, but further work is needed to develop simple predictors of bioavailability of DOC in a range of environments. Consumers of bacteria in streams range in size from protists to insect larvae, with highest rates of bacterial consumption found among the meiofauna and certain filter feeders and grazers. Because there appear to be fewer trophic transfers in the lotic microbial loop, it functions more as a link in flowing waters than it appears to do in the marine plankton.     

Carbon fluxes in the microbial loop: Comments

The heterotrophic bacterial community of oceanic aggregates which mediates particle solubilization, displays features (low carbon demand and low turnover) that are difficult to reconcile with the observed high enzyme activities and cell numbers. Hypotheses are proposed to explain this discrepancy. Furthermore, production of both free and attached bacteria may have been underestimated by neglecting the ultramicrobacteria (UMB). Production of UMB may represent up to 28% of the total bacterial production.     

Climate change feedbacks to microbial decomposition in boreal soils

Boreal ecosystems store 10–20 % of global soil carbon and may warm by 4–7 °C over the next century. Higher temperatures could increase the activity of boreal decomposers and indirectly affect decomposition through other ecosystem feedbacks. For example, permafrost melting will likely alleviate constraints on microbial decomposition and lead to greater soil CO₂ emissions. However, wet boreal ecosystems underlain by permafrost are often CH₄ sources, and permafrost thaw could ultimately result in drier soils that consume CH₄, thereby offsetting some of the greenhouse warming potential of soil CO₂ emissions. Climate change is also likely to increase winter precipitation and snow depth in boreal regions, which may stimulate decomposition by moderating soil temperatures under the snowpack. As temperatures and evapotranspiration increase in the boreal zone, fires may become more frequent, leading to additional permafrost loss from burned ecosystems. Although post-fire decomposition could also increase due to higher soil temperatures, reductions in microbial biomass and activity may attenuate this response. Other feedbacks such as soil drying, increased nutrient mineralization, and plant species shifts are either weak or uncertain. We conclude that strong positive feedbacks to decomposition will likely depend on permafrost thaw, and that climate feedbacks will probably be weak or negative in boreal ecosystems without permafrost. However, warming manipulations should be conducted in a broader range of boreal systems to validate these predictions.     

Interactions between algae and the microbial loop in experimental microcosms

We conducted a short-term microcosm experiment to study the direct and indirect effects of a bacterivore on bacteria and the dynamics of two species of green algae. We introduced Scenedesmus , Chlorella and Colpidium , a bacterivorous ciliate, successively in a carbon-rich medium. Bacteria were introduced with Scenedesmus , Chlorella and Colpidium . The experiment lasted 40 days, preventing us from detecting whether the populations had reached equilibrium. The bacterivore had a positive effect on both species of algae by limiting the abundance of bacteria. In absence of the bacterivore, bacteria did not exclude the two algal species, despite the high carbon:nutrient ratio of the medium. Unexpectedly, by the end of the experiment the bacterivore declined in all microcosms. Also, Chlorella growth was impeded by the presence of Scenedesmus . These two observations might be explained by allelopathic interactions. Our experiment suggests that the functioning of such a simple community is far more complex than assumed in previous theoretical and experimental models. Studying the dynamics of the system, however, allowed us to disentangle species interactions.     

Response of microbial community structure to microbial plugging in a mesothermic petroleum reservoir in China

Microbial plugging, a microbial enhancement of oil recovery (MEOR) technique, has been applied in a candidate oil reservoir of Daqing Oil Field (China). The goal of this study is to monitor the survival of injected bacteria and reveal the response of microbial communities in field trial of microbial plugging through injection of selected microbial culture broth and nutrients. Culture-dependent enrichment and culture-independent 16S rDNA clone library methods were used. The results show that it was easy to activate targeted biopolymer-producing bacteria in a laboratory environment, and it was difficult for injected exogenous bacteria to survive. In addition, microbial communities in the oil reservoir also changed before and after the field trial. However, microbial communities, activated by fermentative medium for biopolymer-producing bacteria, appeared to show greater differences in the laboratory than in the natural reservoir. It was concluded that microbial populations monitoring was important to MEOR; results of response of microbial communities could provide a guide for the future field trials.     

Phagotrophy and NH4+ regeneration in a three-member microbial food loop

In a series of batch experiments we compared the efficiencyof nitrogen regeneration of a two- and three-member microbialfood loop consisting of a mixed bacterial assemblage, a small(3–5 µm) heterotrophic flagellate (Paraphysomonassp.), and a large (7–12 µm) heterotrophic flagellate(Paraphysomonas imperforata). In the two-member system the nitrogenregeneration efficiency for NH₄⁺ (R_n) was 41% and the grossgrowth efficiency (GGE) was 57% during active grazing by thesmall flagellate on bacteria. Regeneration of NH₄⁺ continuedduring the stationary phase so that R_n was 75% after 6 daysincubation. When the larger flagellate was introduced at theend of exponential growth of the smaller grazer in the three-membersystem, initially there was rapid regrowth of bacteria, tyingup 15% of the nitrogen originally in the bacteria. The largerflagellate grazed the smaller one with a GGE of 55%. Total nitrogenregeneration efficiency through exponential growth of the largerflagellate was 73%. Because microbial food loops in naturalwaters are far more complicated and with more grazing stepsthan portrayed in this study, we would expect the bulk of nutrientswithin these systems to be recycled with little transfer tohigher trophic levels.     

Inorganic nutrients,bacteria, and the microbial loop

The realization that natural assemblages of planktonic bacteria may acquire a significant fraction of their nitrogen and phosphorus via the uptake of dissolved inorganic nutrients has modified our traditional view of these microorganisms as nutrient remineralizers in plankton communities. Bacterial uptake of inorganic nitrogen and phosphorus may place bacteria and phytoplankton in competition for growth-limiting nutrients, rather than in their traditional roles as the respective source and sink for these nutrients in the plankton. Bacterial nutrient uptake also implies that bacterivorous protozoa may play a pivotal role in the remineralization of these elements in the microbial loop. The overall contribution of bacterial utilization of inorganic nutrients to total nutrient uptake in the ocean is still poorly understood, but some generalizations are emerging with respect to the geographical areas and community physiological conditions that might elicit this behavior.     

A model of microbial contamination of a water reservoir

A three year record of daily fecal coliform counts in a Massachusetts water reservoir has the appearance of an irregular time series punctuated by outbursts of varying duration. The pattern is described in terms of a probabilistic model where the fluctuations in the ‘regular’ and ‘explosive’ regimes are governed by two sets of probabilities. It has been assumed that the random oscillations has a lognormal distribution, and that once an explosion threshold has been exceeded the increments or decrements in the population size have fixed probability distributions. The threshold for triggering an outburst was estimated by examining the randomness of the autocorrelation function of the record after it is filtered to eliminate peaks of progressively increasing magnitude. Once the threshold has been identified, the mean and standard deviation of the underlying lognormal distribution could be estimated directly from remains found in the record after all the peaks were removed. The probabilities of an increment and decrement during the outbursts and their relative magnitudes could also be estimated using simple formulas. These estimated parameter values were then used to generate realistic records with known threshold levels, which were subsequently used to assess the procedure’s feasibility and sensitivity.     

Filterable microbial forms in the Rybinsk water reservoir

Molecular identification of the filterable forms of microorganisms in the water of the Rybinsk reservoir, one of the largest open water bodies in European Russia, was carried out. The number of ultrasmall microbial cells passing through 0.22 μm filters was 104 cells/mL. These were represented by both bacteria and archaea. Most bacterial 16S rRNA gene sequences retrieved from filtered water affiliated with the Betaproteobacteria and exhibited high similarity (99.0–99.5%) to those of bacteria of the genus Polynucleobacter. The archaeal 16S rRNA gene clone library was composed of the sequences from members of the Euryarchaeota, including the orders Methanobacteriales and Methanomicrobiales, as well as two archaeal groups (LDS and RC-V) with no characterized representatives. The species composition of filterable bacteria from reservoir water was different from that revealed previously in bogs and small lakes at catchment areas. By contrast, the pool of filterable archaea in the reservoir exhibited significant similarity to that at boggy catchment areas and was characterized by predominance of the clade LDS. Available data indicate that this archaeal group is typical of the northern freshwater ecosystems, and the organisms of this group are represented by ultrasmall cells.     

Responses of aerobic microbial communities and soil respiration to water-level drawdown in a northern boreal fen

On a global basis, peatlands are a major reserve of carbon (C). Hydrological changes can affect the decomposition processes in peatlands and in turn can alter their C balance. Since 1959, a groundwater extraction plant has generated a water-level gradient at our study site that has gradually changed part of the wet fen into a dry peatland forest. The average water-level drawdown of the gradient (from a pristine 9 cm to 26 cm in the dry end) is close to an estimate predicted by an increase in mean global temperature of 3°C. We studied the total microbial community of the aerobic surface peat in four locations along the gradient through phospholipid fatty acid and PCR-DGGE methods. Additionally, field measurements of soil respiration showed a threefold increase in the C-emission rate at the driest location compared with the wettest one, indicating enhanced decomposition. Also, both fungal and bacterial biomass increased in the drier locations. At the species level, the fungal community changed due to water-level drawdown whereas actinobacteria were less sensitive to drying. The majority of fungal sequences were similar to ectomycorrhizal (ECM) fungi, which dominated throughout the gradient. Our results indicate that ECM fungi might act as important facultative decomposers in organic-rich environments such as peatlands.