Bacteriophage in polar inland waters

Bacteriophages are found wherever microbial life is present and play a significant role in aquatic ecosystems. They mediate microbial abundance, production, respiration, diversity, genetic transfer, nutrient cycling and particle size distribution. Most studies of bacteriophage ecology have been undertaken at temperate latitudes. Data on bacteriophages in polar inland waters are scant but the indications are that they play an active and dynamic role in these microbially dominated polar ecosystems. This review summarises what is presently known about polar inland bacteriophages, ranging from subglacial Antarctic lakes to glacial ecosystems in the Arctic. The review examines interactions between bacteriophages and their hosts and the abiotic and biotic variables that influence these interactions in polar inland waters. In addition, we consider the proportion of the bacteria in Arctic and Antarctic lake and glacial waters that are lysogenic and visibly infected with viruses. We assess the relevance of bacteriophages in the microbial loop in the extreme environments of Antarctic and Arctic inland waters with an emphasis on carbon cycling.     

Toward the development of generally applicable models of the microbial loop in aquatic ecosystems

Simulation modeling has been an integral, albeit ad hoc, component of the field of aquatic microbial ecology for the past two decades. One of the most critical steps in simulation modeling is the initial formulation of a clear set of questions and goals. It is doubtful that a single generic model could be constructed to address adequately all questions of interest concerning the microbial loop because of the tremendous range in time scales that define these questions. Progress in the field of aquatic microbial ecology will benefit from an integrated research program including experimental and modeling approaches. A submodel of bacterial utilization of various qualities of organic matter that we have under construction is presented. This submodel will be a component of a larger model to evaluate the effects of quality and quantity of organic matter and inorganic nutrient inputs on estuarine food web structure and efficiency. The overall model will be general enough in its structure that it should be applicable to a wide range of questions concerning the microbial loop, with time scales ranging from hours to days.     

Prokaryotes and the input of polyunsaturated fatty acids to the marine food web

The investigation of prokaryotes in aquatic ecology is often limited to their role in nutrient cycling and the degradation of organic matter. While this aspect of the microbial loop is undoubtedly important, further aspects of bacterial roles in marine food webs exist which have not been fully considered in light of recent research in related fields. The concept of bacteria providing essential nutrients may derive importance from two aspects of their role in the marine environment; firstly as a primary food source for omnivorous, sestonivorous and filtering benthic animals and secondly as components of the commensal microbial communities of marine animals. Many marine organisms lack the de novo ability to produce n-3 polyunsaturated fatty acids (PUFA) and hence rely on a dietary supply of PUFA. The issue of PUFA origin in the marine food web is particularly salient in light of recent research demonstrating the influence of PUFA levels on the efficiency of energy transfer between trophic levels. The assumption that microalgae provide the bulk of de novo PUFA production for all marine food webs must be actively reviewed with respect to particular microbial niches such as sea ice, marine animals and abyssal communities.     

Ecology of planktonic heterotrophic flagellates. A review.

In aquatic environments heterotrophic flagellates are an important component within the microbial loop and the food web, owing to their involvement in the energy transfer and flux and as an intermediate link between bacteria and primary producers, and greater organisms, such as other protists and metazoan consumers. In the microbial loop heterotrophic flagellates highly contribute to fast biomass and nutrient recycling and to the production in aquatic environments. In fact, these protists consume efficiently viruses, bacteria, cyanobacteria and picophytoplankton, and are grazed mainly by other protists, rotifers and small crustaceans. In this paper the knowledge about these unicellular organisms is reviewed, taking into particular account their ecological relationships and trophic role within the plankton community of marine and freshwater environments.     

A mini-review of microbial consortia: Their roles in aquatic production and biogeochemical cycling

Molecular oxygen (O₂) is a potent inhibitor of key microbial processes, including photosynthesis, N₂ fixation, denitrification, sulfate reduction, methanogenesis, iron, and metal reduction reactions. Prokaryote survival and proliferation in aquatic environments is often controlled by the ability to tolerate exposure to oxic conditions. Many prokaryotes do not have subcellular organelles for isolating O₂-producing from O₂-consuming processes and have developed consortial associations with other prokaryotes and eukaryotes that alleviate metabolic constraints of high O₂. Nutrient transformations often rely on appropriate cellular and microenvironmental, or microzonal, redox conditions. The spatial and temporal requirements for microenvironmental overlap among microbial groups involved in nutrient transformations necessitates close proximity and diffusional exchange with other biogeochemically distinct, yet complementary, microbial groups. Microbial consortia exist at different levels of community and metabolic complexity, as shown for detrital, microbial mat, biofilm, and planktonic microalgal-bacterial assemblages. To assess the macroscale impacts of consortial interactions, studies should focus on the range of relevant temporal (minutes to hours) and spatial (microns to centimeters) scales controlling microbial production, nutrient exchange, and cycling. In this review, we discuss the utility and application of techniques suitable for determining microscale consortial activity, production, community composition, and interactions in the context of larger scale aquatic ecosystem structure and function. Correspondence to: Hans W. Paerl.     

WETLANDS AS ACCRETING SYSTEMS: NUTRIENT CYCLING IN WETLANDS

SUMMARY

The major concepts involved in nutrient cycling in wetlands are discussed using phosphorus and nitrogen as examples. The differences in nutrient cycling patterns between hydrologically contrasting wetlands, and the significance of fluctuating water levels in wetlands, are stressed. In South Africa, some research into nutrient cycling in submerged aquatic macrophyte communities has been undertaken, but very little information is available on these processes in wetlands dominated by emergent vegetation forms. Generally, the information available on nutrient cycling processes in South African wetlands is of limited applicability to the assessment of nutrient cycling in whole wetland systems. Therefore, rational wetland management strategies require further research on nutrient cycling.     

The effects of mixotrophy on the stability and dynamics of a simple planktonic food web model

Recognition of the microbial loop as an important part of aquatic ecosystems disrupted the notion of simple linear food chains. However, current research suggests that even the microbial loop paradigm is a gross simplification of microbial interactions due to the presence of mixotrophs-organisms that both photosynthesize and graze. We present a simple food web model with four trophic species, three of them arranged in a food chain (nutrients-autotrophs-herbivores) and the fourth as a mixotroph with links to both the nutrients and the autotrophs. This model is used to study the general implications of inclusion of the mixotrophic link in microbial food webs and the specific predictions for a parameterization that describes open ocean mixed layer plankton dynamics. The analysis indicates that the system parameters reside in a region of the parameter space where the dynamics converge to a stable equilibrium rather than displaying periodic or chaotic solutions. However, convergence requires weeks to months, suggesting that the system would never reach equilibrium in the ocean due to alteration of the physical forcing regime. Most importantly, the mixotrophic grazing link seems to stabilize the system in this region of the parameter space, particularly when nutrient recycling feedback loops are included.     

Microbial trophic interactions in aquatic microcosms designed for testing genetically engineered microorganisms: A field comparison

Microcosms may potentially be used as tools for evaluating the fate and effects of genetically engineered microorganisms released into the environment. Extrapolation of data to the field, however, requires that the correspondence between microcosm and field is known. Microbial trophic interactions within the microbial loop were compared quantitatively and qualitatively between field and microcosms containing estuarine water with and without intact sediment cores. The comparison showed that whereas proportions between trophic levels in microcosms were qualitatively similar to those in the field, rates of microbial processes were from 25 to 40% lower in microcosms. Nitrogen cycling was disrupted in microcosms incubated in the dark to eliminate primary production. Examination of the microbial parameters further suggests that sediment in microcosms may be an important factor regulating the bacterial trophic level. These results demonstrate that analysis of microbial trophic interactions is a sensitive method for the field comparison of aquatic microcosms and a potentially useful tool in the risk assessment of genetically engineered microorganisms. Offprint requests to: N. Kroer.     

Ecological and evolutive implications of bacterial defences against predators

Bacterial communities are often heavily consumed by microfaunal predators, such as protozoa and nematodes. Predation is an important cause of mortality and determines the structure and activity of microbial communities in both terrestrial and aquatic ecosystems, and bacteria evolved various defence mechanisms helping them to resist predation. In this review, I summarize known antipredator defence strategies and their regulation, and explore their importance for bacterial fitness in various environmental conditions, and their implications for bacterial evolution and diversification under predation pressure. I discuss how defence mechanisms affect competition and cooperation within bacterial communities. Finally I present some implications of bacterial defence mechanisms for ecosystem services provided by microbial communities, such as nutrient cycling, virulence and the biological control of plant diseases.     

NUTRIENTS IN AFRICAN LAKE ECOSYSTEMS: DO WE KNOW ALL?

SUMMARY

It is nearly sixty years since the first studies were undertaken on the nutrient chemistry of African lakes. There have been numerous studies on the chemical composition of African waters in the intervening years. Yet as recently as five years ago it was stated that little was known about nutrient cycling in lakes. Nutrient ‘species’ simply formed an additional list compiled along with lists of species of algae, zooplankton, aquatic plants and fish. A spate of monographs, papers and reports in recent years, however, has begun to fill some of the gaps in our knowledge of nutrient cycling in African lake ecosystems. This paper reviews the recent literature of nutrients in African lakes from the point of view of nutrient sources, in-lake nutrient kinetics and nutrient sinks, with particular reference to nitrogen and phosphorus, and their cycling rates into and out of various biotic and abiotic compartments. The principle conclusions that can be drawn from the review are as follows:

1. Allochthonous inputs, particularly in terms of external nutrient loading, have been relatively well-studied in recent years, but little is known of autochthonous nutrient inputs, despite numerous observations that nutrient regeneration is likely to be substantial in African lakes.

2. The rôle of microbial processes in nutrient cycling in African lakes is almost totally unknown, except in relation to nitrification and denitrification.

3. Recent studies have begun to examine the kinetics of the uptake of phosphorus by algae in African lakes; nitrogen uptake, other than nitrification, and nutrient release have only rarely been examined.

4. Nutrient uptake and release by aquatic macrophytes is reasonably well known, especially in the ‘nuisance’ weed species.

5. The role of zooplankton, zoobenthos and fish in nutrient cycling in African lakes has largely been ignored.

6. A great deal of study has been devoted to the rôle of abiotic process, particularly at the sediment-water interface, in the nutrient dynamics of African lakes.

As yet, little emphasis has been placed on inter-compartmental exchanges in studies on nutrient cycles but it would appear that these processes are now beginning to receive attention and, as nutrient cycling in African lake ecosystems becomes better known, research will tend toward a more numerical approach.     

The microbial loop concept as used in terrestrial soil ecology studies

Components and processes in the aquatic microbial loop are compared with the composition and functioning of the soil microbial loop. Relative to their bacterial and/or fungal food sources, many of the soil water-film fauna (e.g., protozoa, nematodes) are conspicuous by low biomasses and high turnover rates of carbon and mineral nutrients. Comparisons with production and turnover rates of aerial (pore-inhabiting) fauna are made, and the highly patchy nature of soil microhabitats is shown to be similar to that of aquatic (marine) habitats.     

Effects of land use on the structure and function of leaf‐litter microbial communities in boreal streams

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三江源地区高寒湿地土壤微生物生物量碳氮磷及其化学计量特征

微生物生物量及其化学计量特征是土壤养分循环的重要参数, 对预测气候变化和提高模型准确性及理解陆地生态系统养分循环都起到重要作用。为了明晰高寒生态系统土壤微生物生物量碳(MBC)、微生物生物量氮(MBN)、微生物生物量磷(MBP)浓度及其化学计量特征, 该研究通过在三江源区高寒湿地连续两年的野外调查和室内培养, 分析了50个样点的数据, 探究三江源高寒湿地MBC、MBN、MBP浓度及其化学计量特征, 明确了土壤理化特性和微生物群落特征对其影响。结果表明: (1)三江源高寒湿地MBC、MBN和MBP浓度分别为105.11、3.79和0.78 mmol·kg^-1, MBC:MBN、MBC:MBP、MBN:MBP和MBC:MBN:MBP分别为50.56、184.89、5.42和275:5:1。高寒湿地土壤的MBC浓度显著高于高寒草甸土壤, 而MBN和MBP浓度在高寒湿地和高寒草甸土壤之间没有显著差异; 高寒湿地土壤的MBC:MBN和MBC:MBP显著高于高寒草甸土壤, 而MBN:MBP在高寒湿地和高寒草甸土壤之间差异不显著。(2)土壤理化特性与MBC、MBN和MBP浓度具有显著相关性。土壤含水率与MBC:MBN和MBC:MBP存在显著负相关关系, 而土壤密度与MBC:MBN和MBC:MBP浓度存在显著正相关关系, 土壤全氮含量和MBC:MBP存在显著负相关关系, 而与MBC:MBN的相关关系不显著。土壤理化特性对MBN:MBP的影响不显著。(3)整体而言, 微生物群落结构与MBC、MBN和MBP浓度之间存在显著的相关性。微生物群落结构和MBC:MBN、MBC:MBP的关系是相似的, 总磷脂脂肪酸(PLFA)含量、革兰氏阳性菌、革兰氏阴性菌、细菌、放线菌、丛枝菌根真菌浓度和其他PLFA含量与MBC:MBN和MBC:MBP存在显著负相关关系, 而真菌:细菌与MBC:MBN和MBC:MBP之间存在显著正相关关系, 真菌浓度与MBC:MBN和MBC:MBP之间的相关关系不显著。除丛枝菌根真菌外, MBN:MBP与微生物群落结构均无显著相关关系。     

Testate amoebae and nutrient cycling: peering into the black box of soil ecology

In some areas of ecology and evolution, such as the behavioural ecology of many well-studied bird species, it is increasingly difficult to make surprising new discoveries. However, this is not the case in many areas of soil and/or microbial ecology. Two recent studies suggest that the testate amoebae, a microbial group unfamiliar to most biologists, might play a much larger role in soil nutrient cycling than has hitherto been suspected.     

Global impact of Vibrio cholerae interactions with chitin

The interaction of Vibrio cholerae with chitin exemplifies for microbial ecology a successful bacteria-substrate interaction with complex and significant influence on the lifestyle of the bacterium. Chitin is one of the most abundant polymers on earth and possibly the most abundant in the aquatic environment, where its association with V. cholerae has provided the microorganism with a number of advantages, including food availability, adaptation to environmental nutrient gradients, tolerance to stress and protection from predators. Emergent properties of V. cholerae-chitin interactions occur at multiple hierarchical levels in the environment and include cell metabolic and physiological responses e.g. chemotaxis, cell multiplication, induction of competence, biofilm formation, commensal and symbiotic relationship with higher organisms, cycling of nutrients, and pathogenicity for humans and aquatic animals. As factors mediating virulence of V. cholerae for humans and aquatic animals derive from mechanisms of adaptation to its environment, at different levels of hierarchical scale, V. cholerae interactions with chitin represent a useful model for examination of the role of primary habitat selection in the development of traits that have been identified as virulence factors in human disease.     

Bottom-up regulation of bacterial growth in tropical phytotelm bromeliads

Evaluating the factors that regulate bacterial growth in natural ecosystems is a major goal of modern microbial ecology. Phytotelm bromeliads have been used as model ecosystems in aquatic ecology as they provide many independent replicates in a small area and often encompass a wide range of limnological conditions. However, as far as we know, there has been no attempt to evaluate the main regulatory factors of bacterial growth in these aquatic ecosystems. Here, we used field surveys to evaluate the main bottom-up factors that regulate bacterial growth in the accumulated water of tank bromeliads. Bacterial production, water temperature, water color, chlorophyll-a, and nutrient concentrations were determined for 147 different tank bromeliads in two different samplings. Bromeliad position and the season of sampling were also noted. Bacterial production was explained by ion ammonium concentration and water temperature, but the total variance explained was low (r ² = 0.104). Sampling period and bromeliad position were included in additional models that gave empirical support for predicting bacterial production. Bromeliad water tanks are extremely variable aquatic ecosystems in space (among bromeliads) and time (environmental conditions can change within hours), and it is well known that bacterial production responds rapidly to environmental change. Therefore, we concluded that several factors could independently regulate bacterial growth in phytotelm bromeliads depending on the characteristics of each bromeliad, such as location, amount of detritus, and ambient nutrient concentrations. A clear bottom-up limitation pattern of bacterial production in tropical phytotelm bromeliads was not found. Handling editor: Luigi Naselli-Flores     

Soil microbial and nutrient responses to 7 years of seasonally altered precipitation in a Chihuahuan Desert grassland

Soil microbial communities in Chihuahuan Desert grasslands generally experience highly variable spatiotemporal rainfall patterns. Changes in precipitation regimes can affect belowground ecosystem processes such as decomposition and nutrient cycling by altering soil microbial community structure and function. The objective of this study was to determine if increased seasonal precipitation frequency and magnitude over a 7‐year period would generate a persistent shift in microbial community characteristics and soil nutrient availability. We supplemented natural rainfall with large events (one/winter and three/summer) to simulate increased precipitation based on climate model predictions for this region. We observed a 2‐year delay in microbial responses to supplemental precipitation treatments. In years 3–5, higher microbial biomass, arbuscular mycorrhizae abundance, and soil enzyme C and P acquisition activities were observed in the supplemental water plots even during extended drought periods. In years 5–7, available soil P was consistently lower in the watered plots compared to control plots. Shifts in soil P corresponded to higher fungal abundances, microbial C utilization activity, and soil pH. This study demonstrated that 25% shifts in seasonal rainfall can significantly influence soil microbial and nutrient properties, which in turn may have long‐term effects on nutrient cycling and plant P uptake in this desert grassland.     

Divide and conquer: Spatial and temporal resource partitioning structures benthic cyanobacterial mats

Benthic cyanobacterial mats are increasing in abundance worldwide with the potential to degrade ecosystem structure and function. Understanding mat community dynamics is thus critical for predicting mat growth and proliferation and for mitigating any associated negative effects. Carbon, nitrogen, and sulfur cycling are the predominant forms of nutrient cycling discussed within the literature, while metabolic cooperation and viral interactions are understudied. Although many forms of nutrient cycling in mats have been assessed, the links between niche dynamics, microbial interactions, and nutrient cycling are not well described. Here, we present an updated review on how nutrient cycling and microbial community interactions in mats are structured by resource partitioning via spatial and temporal heterogeneity and succession. We assess community interactions and nutrient cycling at both intramat and metacommunity scales. Additionally, we present ideas and recommendations for research in this area, highlighting top-down control, boundary layers, and metabolic cooperation as important future directions.     

Long- and short-term effects of fire on nitrogen cycling in tallgrass prairie

Fires in the tallgrass prairie are frequent and significantly alter nutrient cycling processes. We evaluated the short-term changes in plant production and microbial activity due to fire and the long-term consequences of annual burning on soil organic matter (SOM), plant production, and nutrient cycling using a combination of field, laboratory, and modeling studies. In the short-term, fire in the tallgrass prairie enhances microbial activity, increases both above-and belowground plant production, and increases nitrogen use efficiency (NUE). However, repeated annual burning results in greater inputs of lower quality plant residues causing a significant reduction in soil organic N, lower microbial biomass, lower N availability, and higher C:N ratios in SOM. Changes in amount and quality of below-ground inputs increased N immobilization and resulted in no net increases in N availability with burning. This response occurred rapidly (e.g., within two years) and persisted during 50 years of annual burning. Plant production at a long-term burned site was not adversely affected due to shifts in plant NUE and carbon allocation. Modeling results indicate that the tallgrass ecosystem responds to the combined changes in plant resource allocation and NUE. No single factor dominates the impact of fire on tallgrass plant production.