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

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Interactions Between Hyphosphere-Associated Bacteria and the Fungus <Emphasis Type="Italic">Cladosporium herbarum</Emphasis> on Aquatic Leaf Litter

We investigated microbial interactions of aquatic bacteria associated with hyphae (the hyphosphere) of freshwater fungi on leaf litter. Bacteria were isolated directly from the hyphae of fungi from sedimented leaves of a small stream in the National Park “Lower Oder,” Germany. To investigate interactions, bacteria and fungi were pairwise co-cultivated on leaf-extract medium and in microcosms loaded with leaves. The performance of fungi and bacteria was monitored by measuring growth, enzyme production, and respiration of mono- and co-cultures. Growth inhibition of the fungus Cladosporium herbarum by Ralstonia pickettii was detected on leaf extract agar plates. In microcosms, the presence of Chryseobacterium sp. lowered the exocellulase, endocellulase, and cellobiase activity of the fungus. Additionally, the conversion of leaf material into microbial biomass was retarded in co-cultures. The respiration of the fungus was uninfluenced by the presence of the bacterium.     

Temporal and stoichiometric patterns of algal stimulation of litter-associated heterotrophic microbial activity

1. Periphyton communities associated with submerged plant detritus contain interacting autotrophic and heterotrophic microbes, and are sites of extracellular enzymatic activity. The strength and nature of these interactions might be expected to change over time as microbial communities develop on plant litter. Microbial interactions and enzymatic activity can be altered by nutrient availability, suggesting that litter stoichiometry could also affect these phenomena.
2. We grew wetland plants under ambient and nutrient-enriched conditions to generate plant litter of differing nutrient content. In two experiments, we investigated: (1) the influence of algal photosynthesis on fungal and bacterial production and the activities of four extracellular enzymes throughout a 54-day period of microbial colonisation and growth; and (2) the influence of litter stoichiometry on these relationships.
3. Ambient and nutrient-enriched standing-dead plant litter was collected and then submerged in wetland pools to allow for natural microbial colonisation and growth. Litter samples were periodically retrieved and transported to the laboratory for experiments manipulating photosynthesis using the photosystem II inhibitor DCMU (which effectively prevents algal photosynthetic activity). Algal (¹⁴C-bicarbonate), bacterial (³H-leucine), and fungal (¹⁴C-acetate) production, and β-glucosidase, β-xylosidase, leucine aminopeptidase, and phosphatase activities (MUF- or AMC-labelled fluorogenic substrates) were measured under conditions of active and inhibited algal photosynthesis.
4. Photosynthesis stimulated overall fungal and bacterial production in both experiments, although the strength of stimulation varied amongst sampling dates. Phosphatase activity was stimulated by photosynthesis during the first, but not the second, experiment. No other enzymatic responses to short-term photosynthesis manipulations were observed.
5. Microbial communities on high-nutrient litter occasionally showed increased extracellular enzyme activity, fungal growth rates, and bacterial production compared to communities on non-enriched litter, but algal and fungal production were not affected. Litter stoichiometry had no effects on fungal, bacterial, or enzymatic responses to photosynthesis, but the mean enzyme vector analysis angle (a measure of P- versus N-acquiring enzyme activity) was positively correlated to litter N:P, suggesting that elevated litter N:P led to an increase in the relative activity of P-acquiring enzymes.
6. These results supported the hypothesis that algal photosynthesis strongly influences heterotrophic microbial activity on macrophyte leaf litter, especially that of fungi, throughout microbial community development. However, the strength of this photosynthetic stimulation does not generally depend on small differences in litter nutrient content.
7. Stimulation of microbial heterotrophs by algal photosynthesis could drive diurnal shifts in periphyton community and aquatic ecosystem function, as well as linking green (photoautotroph-based) and brown (detrital-based) food webs.

     

Do leaf-litter decomposers control biofilm primary production and benthic algal community structure in forest streams? Insights from an outdoor mesocosm experiment

• 1. Forested headwater streams are generally considered to be light-limited ecosystems where primary production is reduced, and the main source of energy and nutrients is composed of allochthonous detritus. We hypothesised that in these ecosystems, the development of primary producers might also be limited by (1) competition for nutrients with leaf-litter decomposers (e.g. bacteria and fungi), and (2) leaf-litter leachates or allelopathic compounds produced by aquatic fungi.
• 2. To test these hypotheses, a 48-day mesocosm experiment was performed in 12 artificial streams containing stream water inoculated with epilithic biofilm suspensions collected from a forested headwater stream. Three different treatments were applied: control without leaf litter (C), microbially conditioned leaf litter added at the beginning of the experiment and left to decompose throughout the experiment (L), or leaf litter renewed three times during the experiment (RL).
• 3. We predicted that (1) the presence of litter, through microbial nutrient immobilisation and allelopathy, would reduce primary production and that (2) this effect would be amplified by litter renewal. We also predicted that nutrient competition would mean that (3) leaf-litter decomposers will alter primary producer community composition and physiology. These predictions were tested by analysing biofilm development, physiology, stoichiometry, and benthic algal community structure. To distinguish between the effects of nutrient immobilisation and allelopathy, the biofilm responses to leaf-litter leachates collected after different microbial conditioning durations were also measured in a parallel laboratory experiment.
• 4. Contrary to our expectations, by day 28, primary producer growth was higher in the mesocosms containing leaf litter (L and RL) despite the rapid decrease in dissolved nutrients when leaf litter was present. After 48 days, the lowest phototrophic biofilm development was observed when leaf litter was renewed (RL), whereas phototrophic biofilm development was similar in the C and L treatments. Biofilm stoichiometry indicated that this effect was most probably related to greater nitrogen limitation in the RL treatment. The presence of leaf litter also affected primary producers' photophysiology, which could be attributed to changes in taxonomic composition and to physiological adjustments of primary producers.
• 5. Laboratory measurements showed that despite a strong inhibition of primary producer growth by unconditioned leaf-litter leachates, microbially conditioned leaf litter had either low or no effects on the development of primary producers.
• 6. These results reveal that leaf-litter decomposers can have both positive and negative effects on primary producers underlining the need to consider microbial interactions when investigating the functioning of forested headwater streams.

     

Does mixing litter of different qualities alter stream microbial diversity and functioning on individual litter species?

We examined effects of leaf litter quality and species mixing on microbial community diversity and litter processing in a forested headwater stream. Single- and mixed-species litter from dominant tree species ( Liriodendron tulipifera , Acer rubrum , Quercus prinus , Rhododendron maximum ) were incubated in a southern Appalachian headwater stream. Litter carbon-to-nitrogen ratios (C:N), mass loss, microbial respiration, and microbial community diversity were analyzed on individual litter species after incubation. Initial C:N varied widely among individual litter species, and these differences persisted throughout the 50-day incubation period. Litter C:N of the recalcitrant species R. maximum remained higher than that of all other litter species, and C:N of R. maximum and L. tulipifera increased when both species were present together in a mixture. Although mass loss of individual species was generally unaffected by mixing, microbial respiration was greater on A. rubrum and Q. prinus litter incubated with R. maximum compared to either species alone. Enhanced resource heterogeneity, which was experimentally achieved by litter mixing low- and higher-quality litter species, resulted in apparent shifts in microbial community diversity on individual litter species. Responses of bacterial and fungal community diversity to litter mixing varied among individual litter species. Our results suggest that changes in tree species composition in riparian forests and subsequent changes in litter resource heterogeneity could alter stream microbial community diversity and function. As bacteria and fungi are important decomposers of plant litter in aquatic ecosystems, resource-dependent changes in microbial communities could alter detrital processing dynamics in streams.     

Significance of predation by protists in aquatic microbial food webs

Predation in aquatic microbial food webs is dominated by phagotrophic protists, yet these microorganisms are still understudied compared to bacteria and phytoplankton. In pelagic ecosystems, predaceous protists are ubiquitous, range in size from 2 μm flagellates to >100 μm ciliates and dinoflagellates, and exhibit a wide array of feeding strategies. Their trophic states run the gamut from strictly phagotrophic, to mixotrophic: partly autotrophic and partly phagotrophic, to primarily autotrophic but capable of phagotrophy. Protists are a major source of mortality for both heterotrophic and autotrophic bacteria. They compete with herbivorous meso- and macro-zooplankton for all size classes of phytoplankton. Protist grazing may affect the rate of organic sinking flux from the euphotic zone. Protist excretions are an important source of remineralized nutrients, and of colloidal and dissolved trace metals such as iron, in aquatic systems. Work on predation by protists is being facilitated by methodological advances, e.g., molecular genetic analysis of protistan diversity and application of flow cytometry to study population growth and feeding rates. Examples of new research areas are studies of impact of protistan predation on the community structure of prey assemblages and of chemical communication between predator and prey in microbial food webs. This revised version was published online in August 2006 with corrections to the Cover Date.     

Effect of Leaf Type and Pesticide Exposure on Abundance of Bacterial Taxa in Mosquito Larval Habitats

Lentic freshwater systems including those inhabited by aquatic stages of mosquitoes derive most of their carbon inputs from terrestrial organic matter mainly leaf litter. The leaf litter is colonized by microbial communities that provide the resource base for mosquito larvae. While the microbial biomass associated with different leaf species in container aquatic habitats is well documented, the taxonomic composition of these microbes and their response to common environmental stressors is poorly understood. We used indoor aquatic microcosms to determine the abundances of major taxonomic groups of bacteria in leaf litters from seven plant species and their responses to low concentrations of four pesticides with different modes of action on the target organisms; permethrin, malathion, atrazine and glyphosate. We tested the hypotheses that leaf species support different quantities of major taxonomic groups of bacteria and that exposure to pesticides at environmentally relevant concentrations alters bacterial abundance and community structure in mosquito larval habitats. We found support for both hypotheses suggesting that leaf litter identity and chemical contamination may alter the quality and quantity of mosquito food base (microbial communities) in larval habitats. The effect of pesticides on microbial communities varied significantly among leaf types, suggesting that the impact of pesticides on natural microbial communities may be highly complex and difficult to predict. Collectively, these findings demonstrate the potential for detritus composition within mosquito larval habitats and exposure to pesticides to influence the quality of mosquito larval habitats.     

Establishment of Microbial Eukaryotic Enrichment Cultures from a Chemically Stratified Antarctic Lake and Assessment of Carbon Fixation Potential

Lake Bonney is one of numerous permanently ice-covered lakes located in the McMurdo Dry Valleys, Antarctica. The perennial ice cover maintains a chemically stratified water column and unlike other inland bodies of water, largely prevents external input of carbon and nutrients from streams. Biota are exposed to numerous environmental stresses, including year-round severe nutrient deficiency, low temperatures, extreme shade, hypersalinity, and 24-hour darkness during the winter ¹. These extreme environmental conditions limit the biota in Lake Bonney almost exclusively to microorganisms ².Single-celled microbial eukaryotes (called "protists") are important players in global biogeochemical cycling ³ and play important ecological roles in the cycling of carbon in the dry valley lakes, occupying both primary and tertiary roles in the aquatic food web. In the dry valley aquatic food web, protists that fix inorganic carbon (autotrophy) are the major producers of organic carbon for organotrophic organisms ^{4, 2}. Phagotrophic or heterotrophic protists capable of ingesting bacteria and smaller protists act as the top predators in the food web ⁵. Last, an unknown proportion of the protist population is capable of combined mixotrophic metabolism ^{6, 7}. Mixotrophy in protists involves the ability to combine photosynthetic capability with phagotrophic ingestion of prey microorganisms. This form of mixotrophy differs from mixotrophic metabolism in bacterial species, which generally involves uptake dissolved carbon molecules. There are currently very few protist isolates from permanently ice-capped polar lakes, and studies of protist diversity and ecology in this extreme environment have been limited ^{8, 4, 9, 10, 5}. A better understanding of protist metabolic versatility in the simple dry valley lake food web will aid in the development of models for the role of protists in the global carbon cycle.We employed an enrichment culture approach to isolate potentially phototrophic and mixotrophic protists from Lake Bonney. Sampling depths in the water column were chosen based on the location of primary production maxima and protist phylogenetic diversity ^{4, 11}, as well as variability in major abiotic factors affecting protist trophic modes: shallow sampling depths are limited for major nutrients, while deeper sampling depths are limited by light availability. In addition, lake water samples were supplemented with multiple types of growth media to promote the growth of a variety of phototrophic organisms.RubisCO catalyzes the rate limiting step in the Calvin Benson Bassham (CBB) cycle, the major pathway by which autotrophic organisms fix inorganic carbon and provide organic carbon for higher trophic levels in aquatic and terrestrial food webs ¹². In this study, we applied a radioisotope assay modified for filtered samples ¹³ to monitor maximum carboxylase activity as a proxy for carbon fixation potential and metabolic versatility in the Lake Bonney enrichment cultures.     

Closely related protist strains have different grazing impacts on natural bacterial communities

Heterotrophic protists are abundant in most environments and exert a strong top‐down control on bacterial communities. However, little is known about how selective most protists are with respect to their bacterial prey. We conducted feeding trials using cercomonad and glissomonad Cercozoa by assaying them on a standardized, diverse bacterial community washed from beech leaf litter. For each of the nine protist strains assayed here, we measured several phenotypic traits (cell volume, speed, plasticity and protist cell density) that we anticipated would be important for their feeding ecology. We also estimated the genetic relatedness of the strains based on the 18S rRNA gene. We found that the nine protist strains had significantly different impacts on both the abundance and the composition of the bacterial communities. Both the phylogenetic distance between protist strains and differences in protist strain traits were important in explaining variation in the bacterial communities. Of the morphological traits that we investigated, protist cell volume and morphological plasticity (the extent to which cells showed amoeboid cell shape flexibility) were most important in determining bacterial community composition. The results demonstrate that closely related and morphologically similar protist species can have different impacts on their prey base.     

Differential responses of soil bacteria,fungi, archaea and protists to plant species richness and plant functional group identity

Plants are known to influence belowground microbial community structure along their roots, but the impacts of plant species richness and plant functional group (FG) identity on microbial communities in the bulk soil are still not well understood. Here, we used 454‐pyrosequencing to analyse the soil microbial community composition in a long‐term biodiversity experiment at Jena, Germany. We examined responses of bacteria, fungi, archaea, and protists to plant species richness (communities varying from 1 to 60 sown species) and plant FG identity (grasses, legumes, small herbs, tall herbs) in bulk soil. We hypothesized that plant species richness and FG identity would alter microbial community composition and have a positive impact on microbial species richness. Plant species richness had a marginal positive effect on the richness of fungi, but we observed no such effect on bacteria, archaea and protists. Plant species richness also did not have a large impact on microbial community composition. Rather, abiotic soil properties partially explained the community composition of bacteria, fungi, arbuscular mycorrhizal fungi (AMF), archaea and protists. Plant FG richness did not impact microbial community composition; however, plant FG identity was more effective. Bacterial richness was highest in legume plots and lowest in small herb plots, and AMF and archaeal community composition in legume plant communities was distinct from that in communities composed of other plant FGs. We conclude that soil microbial community composition in bulk soil is influenced more by changes in plant FG composition and abiotic soil properties, than by changes in plant species richness per se.     

Two microcrustaceans affect microbial and macroinvertebrate‐driven litter breakdown

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The importance of bacterivorous protists in the decomposition of stream leaf litter

1. Allochthonous organic matter, in the form of senesced leaves, is a major source of carbon supporting detrital food webs. While studies have documented the role of bacteria and fungi in the decomposition of leaf litter, little information is available regarding the role of protists in the decomposition process. 2. We tested the hypothesis that the presence of stream‐dwelling bacterivorous protists leads to an increased rate of leaf decomposition through grazing pressure on bacteria. We isolated live protists from decomposing leaves collected in a stream in Northern Virginia, U.S.A. (Goose Creek) and established laboratory cultures of common bacterivorous protists. 3. Recently senesced leaves from the field were used in laboratory microcosm experiments to determine if the rate of litter decomposition differed between four treatments: bacteria only, bacteria + flagellates, bacteria + flagellates + ciliates, autoclaved stream water (control). We determined the dry weight of leaf remaining, bacterial abundance, flagellate abundance and ciliate abundance for each replicate on days 0, 7, 14, 30, 60 and 120. 4. The rate of leaf decomposition was significantly higher in treatments with protists than without and bacterial abundance declined in protist treatments compared with bacteria only treatment. Weight loss in the presence of flagellates was three to four times higher when protists were present compared with treatments with bacteria alone. These results provide experimental evidence that protists could play a significant role in the detrital processes of streams.     

Effects of invasive clam (Corbicula fluminea) die‐offs on the structure and functioning of freshwater ecosystems

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Diversity,role in decomposition,and succession of zoosporic fungi and straminipiles on submerged decaying leaves in a woodland stream

Leaf litter is a very important primary source of energy in woodland streams. Decomposition of leaf litter is a process mediated by many groups of microorganisms which release extracellular enzymes for the degradation of complex macromolecules. In this process, true fungi and straminipiles are considered to be among the most active groups, more active than the bacteria, at least during the early stages of the process. Colonization increases the quality of the leaves as a food resource for detritivores. In this way, matter and energy enter detritus-based food chains. Previously, aquatic hyphomycetes were considered to be the major fungal group responsible for leaf litter decomposition. Although zoosporic fungi and straminipiles are known to colonize and decompose plant tissues in various environments, there is scant information on their roles in leaf decomposition. This study focuses on the communities of zoosporic fungi and straminipiles in a stream which are involved in the decomposition of leaves of two plant species, Ligustrum lucidum and Pouteria salicifolia, in the presence of other groups of fungi. A characteristic community dominated by Nowakowskiella elegans, Phytophthora sp., and Pythium sp. was found. Changes in the fungal community structure over time (succession) was observed: terrestrial mitosporic fungi appeared during the early stages, zoosporic fungi, straminipiles, and aquatic Hyphomycetes in early-to-intermediate stages, while representatives of the phylum Zygomycota were found at early and latest stages of the decomposition. These observations highlight the importance of zoosporic fungi and straminipiles in aquatic ecosystems.     

Channeling of bacterioplanktonic production toward phagotrophic flagellates and ciliates under different seasonal conditions in a river

The objective of this study was to analyze the flux of biomass through the communities of bacteria and phagotrophic protists in the cold and warm conditions occurring seasonally in Butrón River. Bacterial and heterotrophic protistan (flagellate and ciliate) abundance was determined by epifluorescence direct counts; protistan grazing on planktonic bacteria was measured from fluorescently labeled bacteria uptake rates; and the estimate of bacterial secondary production was obtained from [³H]thymidine incorporation rates. The abundance of bacterial, flagellate, and ciliate communities was similar during cold and warm situations. However, we observed that estimates of dynamic parameters, i.e., secondary bacterial production and protistan grazing, in both situations were noticeably different. In the warm situation, grazing rates of flagellates and ciliates (bacteria per protist per hour) were, respectively, 7 times and 18 times higher than those determined in the cold situation, and the grazing rates of the protistan communities (bacteria per protists present in 1 ml of water per hour) increased up to 5 times in the case of flagellates and 42 times in the case of ciliates. Estimates of bacterial secondary production were also higher during the warm situation, showing a ninefold increase. The percentage of bacterial production preyed upon by flagellates or ciliates was not significantly different between the two conditions. These results showed that in the different conditions of a system, the flux of biomass between the trophic levels may be quite different although this process may not be reflected in the abundance of each community of bacteria, flagellates, and ciliates. Offprint requests to: J. Iriberri.     

An analysis of protists in Pacific oxygen deficient zones: implications for Prochlorococcus and N2-producing bacteria

Ocean oxygen deficient zones (ODZs) host 30%–50% of marine N₂ production. Cyanobacteria photosynthesizing in the ODZ create a secondary chlorophyll maximum and provide organic matter to N₂-producing bacteria. This chlorophyll maximum is thought to occur due to reduced grazing in anoxic waters. We first examine ODZ protists with long amplicon reads. We then use non-primer-based methods to examine the composition and relative abundance of protists in metagenomes from the Eastern Tropical North and South Pacific ODZs and compare these data to the oxic Hawaii Ocean Time-series (HOT) in the North Pacific. We identify and quantify protists in proportion to the total microbial community. From metagenomic data, we see a large drop in abundance of fungi and protists such as choanoflagellates, radiolarians, cercozoa and ciliates in the ODZs but not in the oxic mesopelagic at HOT. Diplonemid euglenozoa were the only protists that increased in the ODZ. Dinoflagellates and foraminifera reads were also present in the ODZ though less abundant compared to oxic waters. Denitrification has been found in foraminifera but not yet in dinoflagellates. DNA techniques cannot separate dinoflagellate cells and cysts. Metagenomic analysis found taxonomic groups missed by amplicon sequencing and identified trends in abundance.     

Key role of streambed moisture and flash storms for microbial resistance and resilience to long‐term drought

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Fungal endophyte‐infected leaf litter alters in‐stream microbial communities and negatively influences aquatic fungal sporulation

Endophytes are ubiquitous plant‐associated microbes and although they have the potential to alter the decomposition of infected leaf litter, this has not been well‐studied. The endophyte Rhytisma punctatum infects the leaves of Acer macrophyllum (bigleaf maple), causing the appearance of black ‘tar spots’ that persist in senesced leaves. Other foliar fungi also cause visible damage in healthy tissues of this host plant system including an unidentified bullseye‐shaped lesion, common in western Washington. Using three treatments of endophyte infection status in leaf tissue (R. punctatum‐infected, bullseye‐infected, lesion‐free), leaf litter discs were submerged in a third‐order temperate stream using mesh litter bags and harvested periodically over two months to determine the effects of litter treatment and incubation time on litter mass loss, fungal sporulation, and microbial community colonization. Litter containing symptomatic endophyte infections (Rhytisma or bullseye) had reduced sporulation of aquatic hyphomycetes, but decomposed significantly faster than lesion‐free or bullseye‐infected litter. Using amplicon‐based sequencing, we found a significant difference in bacterial communities colonizing Rhytisma‐infected and bullseye‐infected leaf litter, a significant difference in fungal communities colonizing Rhytisma‐infected leaf litter compared to the two other treatments, and a change in both community structure and relative abundances of bacterial and fungal taxa throughout the study period. Indicator Species Analysis clarified the drivers of these community shifts at the genus level. Our results show that endophyte‐associated, in‐stream sporulation and microbial community effects are observable within one species of leaf litter.     

Assessing the influence of wildfire on leaf decomposition and macroinvertebrate communities in boreal streams using mixed-species leaf packs

1. We investigated how compositional differences in riparian leaf litter derived from burned and undisturbed forests influenced leaf breakdown and macroinvertebrate communities using experimental mixed-species leaf packs in boreal headwater streams. Leaf pack mixtures simulating leaf litter from dominant riparian woody-stem species in burned and undisturbed riparian zones were incubated in two references and two fire-disturbed streams for 5 weeks prior to measuring temperature-corrected breakdown rates and macroinvertebrate community composition, richness, and functional metrics associated with decomposers such as shredder abundance and % shredders.
2. Leaf litter breakdown rates were higher and had greater variability in streams bordered by reference riparian forests than in streams where riparian forests had been burned during a wildfire. Streams bordered by fire disturbance showed significant effects of litter mixture on decomposition rates, observed as significantly higher decomposition rates of a fire-simulated leaf mixture compared to all other mixtures.
3. Variation among sites was higher than variation among litter mixtures, especially for macroinvertebrate community composition. In general, fire-simulated leaf mixtures had greater shredder abundances and proportions, but lower overall macroinvertebrate abundance; however, the shredder abundance trend was not consistent across all leaf mixtures at each stream.
4. These results show that disturbance-driven riparian forest condition and resulting composition of leaf subsidies to streams can influence aquatic invertebrate community composition and their function as decomposers. Therefore, if one of the primary goals of modern forest management is to emulate natural disturbance patterns, boreal forest managers should adapt silvicultural practices to promote leaf litter input that would arise post-fire, thereby supporting stream invertebrate communities and their function.

     

It is about time: genetic variation in the timing of leaf‐litter inputs influences aquatic ecosystems

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