Abstract
The physiology, biochemistry and diversity of aquatic microbial decomposers have been largely investigated in low-order streams. However, some aspects still need further attention to better ascertain how microbial decomposer diversity can ensure ecosystem processes and services, particularly under the challenges posed by global environmental change. Aquatic microbial decomposers play a key role in processing plant litter in streams by degrading the most recalcitrant compounds and facilitating nutrient and energy transfer to higher trophic levels. Among microbial decomposers, fungi, particularly aquatic hyphomycetes, play a fundamental role at the early stages of plant litter decomposition, while the relevance of bacteria increases at the late stage of the decomposition. High-throughput sequencing and metagenomic techniques open new avenues towards a more comprehensive understanding of microbial decomposer ecology. This chapter provides a general overview of aquatic microbial diversity and activity on decomposing plant litter. Attention will be paid to the relationships between microbial diversity and their ecological functions under the major threats posed by the ongoing global environmental change to provide the response patterns of microbial decomposers to maintain nutrient and energy fluxes in streams.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Abelho, M. (2009). ATP and ergosterol as indicators of fungal biomass during leaf decomposition in streams: A comparative study. International Review of Hydrobiology, 94, 3–15.
Abelho, M. (2020). ATP as a measure of microbial biomass. In M. A. S. Graça, F. Bärlocher, & M. O. Gessner (Eds.), Methods to study litter decomposition: A practical guide (pp. 291–299). Springer.
Abelho, M., & Graça, M. A. S. (2006). Effects of nutrient enrichment on decomposition and fungal colonization of sweet chestnut leaves in an Iberian stream (Central portugal). Hydrobiologia, 560, 239–247.
Amani, M., Graça, M. A. S., & Ferreira, V. (2019). Effects of elevated atmospheric CO2 concentration and temperature on litter decomposition in streams: A meta-analysis. International Review of Hydrobiology, 104, 14–25.
Anderson, J. L., & Shearer, C. A. (2011). Population genetics of the aquatic fungus Tetracladium marchalianum over space and time. PLoS ONE, 6, e15908.
Andrade, R., Pascoal, C. & Cássio, F. (2016) Effects of inter and intraspecific diversity and genetic divergence of aquatic fungal communities on leaf litter decomposition—a microcosm experiment. FEMS Microbiology Ecology, 92, 1–18.
Arce Funck, J., Bec, A., Perrière, F., Felten, V., & Danger, M. (2015). Aquatic hyphomycetes: A potential source of polyunsaturated fatty acids in detritus-based stream food webs. Fungal Ecology, 13, 205–210.
Arsuffi, T. L., & Suberkropp, K. (1984). Leaf processing capabilities of aquatic hyphomycetes—Interspecific differences and influence on shredder feeding preferences. Oikos, 42, 144–154.
Arsuffi, T. L., & Suberkropp, K. (1985). Selective feeding by stream caddisfly (Trichoptera) detritivores on leaves with fungal-colonized patches. Oikos, 45, 50–58.
Arsuffi, T. L., & Suberkropp, K. (1986). Growth of two stream caddisflies (Trichoptera) on leaves colonized by different fungal species. Journal of the North American Benthological Society, 5, 297–305.
Artigas, J., Majerholc, J., Foulquier, A., Margoum, C., Volat, B., Neyra, M., & Pesce, S. (2012). Effects of the fungicide tebuconazole on microbial capacities for litter breakdown in streams. Aquatic Toxicology, 122, 197–205.
Artigas, J., Romaní, A. M., & Sabater, S. (2008). Effect of nutrients on the sporulation and diversity of aquatic hyphomycetes on submerged substrata in a Mediterranean stream. Aquatic Botany, 88, 32–38.
Baldy, V., Chauvet, E., Charcosset, J.-Y., & Gessner, M. O. (2002). Microbial dynamics associated with leaves decomposing in the mainstem and floodplain pond of a large river. Aquatic Microbial Ecology, 28, 25–36.
Baldy, V., Gessner, M. O., & Chauvet, E. (1995). Bacteria, fungi and the breakdown of leaf litter in a large river. Oikos, 74, 93–102.
Balian, E. V., Segers, H., Lévèque, C., & Martens, K. (2008). The freshwater animal diversity assessment: An overview of the results. Hydrobiologia, 595, 627–637.
Barajas-Aceves, M., Hassan, M., Tinoco, R., & Vazquez-Duhalt, R. (2002). Effect of pollutants on the ergosterol content as indicator of fungal biomass. Journal of Microbiological Methods, 50, 227–236.
Bärlocher, F. (1982). Conidium production from leaves and needles in four streams. Canadian Journal of Botany, 60, 1487–1494.
Bärlocher, F. (1992). The ecology of aquatic hyphomycetes. Springer-Verlag.
Bärlocher, F. (2000). Water-borne conidia of aquatic hyphomycetes: Seasonal and yearly patterns in Catamaran Brook, New Brunswick, Canada. Canadian Journal of Botany-Revue Canadienne De Botanique, 78, 157–167.
Bärlocher, F. (2007). Molecular approaches applied to aquatic hyphomycetes. Fungal Biology Reviews, 21, 19–24.
Bärlocher, F. (2009). Reproduction and dispersal in aquatic hyphomycetes. Mycoscience, 50, 3–8.
Bärlocher, F. (2010). Molecular approaches promise a deeper and broader understanding of the evolutionary ecology of aquatic hyphomycetes. Journal of the North American Benthological Society, 29, 1027–1041.
Bärlocher, F. (2020). Sporulation by aquatic hyphomycetes. In F. Bärlocher, M. O. Gessner, & M. A. S. Graça (Eds.), Methods to study litter decomposition. (pp. 241–245). Springer.
Bärlocher, F., & Corkum, M. (2003). Nutrient enrichment overwhelms diversity effects in leaf decomposition by stream fungi. Oikos, 101, 247–252.
Bärlocher, F., & Graça, M. A. S. (2002). Exotic riparian vegetation lowers fungal diversity but not leaf decomposition in Portuguese streams. Freshwater Biology, 47, 1123–1135.
Bärlocher, F., Seena, S., Wilson, K. P., & Williams, D. D. (2008). Raised water temperature lowers diversity of hyporheic aquatic hyphomycetes. Freshwater Biology, 53, 368–379.
Barros, D., Pradhan, A., Pascoal, C., & Cássio, F. (2020). Proteomic responses to silver nanoparticles vary with the fungal ecotype. Science of the Total Environment, 704, 135385.
Baschien, C. (2003). Development an evaluation of rRNA targeted in situ probes and phylogenetic relationships of freshwater fungi (PhD thesis). Technischen Universität Berlin.
Baschien, C., Manz, W., Neu, T. R., & Szewzyk, U. (2001). Fluorescence in situ hybridization of freshwater fungi. International Review of Hydrobiology, 86, 371–381.
Baschien, C., Marvanova, L., & Szewzyk, U. (2006). Phylogeny of selected aquatic hyphomycetes based on morphological and molecular data. Nova Hedwigia, 83, 311–352.
Baschien, C., Tsui, C.K.-M., Gulis, V., Szewzyk, U., & Marvanová, L. (2013). The molecular phylogeny of aquatic hyphomycetes with affinity to the Leotiomycetes. Fungal Biology, 117, 660–672.
Batista, D., Tlili, A., Gessner, M. O., Pascoal, C., & Cássio, F. (2020). Nanosilver impacts on aquatic microbial decomposers and litter decomposition assessed as pollution-induced community tolerance (PICT). Environmental Science: Nano, 7, 2130–2139.
Baudy, P., Konschak, M., Sakpal, H., Baschien, C., Schulz, R., Bundschuh, M. & Zubrod, J.P. (2020). The fungicide tebuconazole confounds concentrations of molecular biomarkers estimating fungal biomass. Bulletin of Environmental Contamination and Toxicology, in press.
Baudy, P., Zubrod, J. P., Röder, N., Baschien, C., Feckler, A., Schulz, R., & Bundschuh, M. (2019). A glance into the black box: Novel species-specific quantitative real-time PCR assays to disentangle aquatic hyphomycete community composition. Fungal Ecology, 42, 100858.
Bauer, R., Begerow, D., Oberwinkler, F., & Marvanová, L. (2003). Classicula: The teleomorph of Naiadella fluitans. Mycologia, 95, 756–764.
Belliveau, M. J. R., & Bärlocher, F. (2005). Molecular evidence confirms multiple origins of aquatic hyphomycetes. Mycological Research, 109, 1407–1417.
Bergmann, M., & Graça, M. A. S. (2020). Uranium affects growth, sporulation, biomass and leaf-litter decomposition by aquatic hyphomycetes. Limnetica, 39, 141–154.
Bermingham, S., Dewey, F. M., Fisher, P. J., & Maltby, L. (2001). Use of a monoclonal antibody-based immunoassay for the detection and quantification of Heliscus lugdunensis colonizing alder leaves and roots. Microbial Ecology, 42, 506–512.
Bermingham, S., Dewey, F. M., & Maltby, L. (1995). Development of a monoclonal antibody-based immunoassay for the detection and quantification of Anguillospora longissima colonizing leaf material. Applied and Environmental Microbiology, 61, 2606–2613.
Bermingham, S., Maltby, L., & Dewey, F. M. (1996). Monoclonal antibodies as tools to quantify mycelium of aquatic hyphomycetes. New Phytologist, 132, 593–601.
Bermingham, S., Maltby, L., & Dewey, F. M. (1997). Use of immunoassays for the study of natural assemblages of aquatic hyphomycetes. Microbial Ecology, 33, 223–229.
Boyero, L., Pearson, R. G., Gessner, M. O., Barmuta, L. A., Ferreira, V., Graça, M. A. S., Dudgeon, D., Boulton, A. J., Callisto, M., Chauvet, E., Helson, J. E., Bruder, A., Albariño, R. J., Yule, C. M., Arunachalam, M., Davies, J. N., Figueroa, R., Flecker, A. S., Ramírez, A., … West, D. C. (2011). A global experiment suggests climate warming will not accelerate litter decomposition in streams but might reduce carbon sequestration. Ecology Letters, 14, 289–294.
Buesing, N., & Gessner, M. O. (2020). Bacterial abundance and biomass determination in plant litter by epifluorescence microscopy. In F. Bärlocher, M. O. Gessner, & M. A. S. Graça (Eds.), Methods to study litter decomposition (pp. 265–273). Springer.
Campbell, J., Marvanová, L., & Gulis, V. (2009). Evolutionary relationships between aquatic anamorphs and teleomorphs: Tricladium and Varicosporium. Mycological Research, 113, 1322–1334.
Campbell, J., Shearer, C., & Marvanova, L. (2006). Evolutionary relationships among aquatic anamorphs and teleomorphs: Lemonniera, Margaritispora, and Goniopila. Mycological Research, 110, 1025–1033.
Canhoto, C., & Graça, M. A. S. (1996). Decomposition of Eucalyptus globulus leaves and three native leaf species (Alnus glutinosa, Castanea sativa and Quercus faginea) in a Portuguese low order stream. Hydrobiologia, 333, 79–85.
Carlisle, D. M., & Clements, W. H. (2005). Leaf litter breakdown, microbial respiration and shredder production in metal-polluted streams. Freshwater Biology, 50, 380–390.
Chapin, F. S., III., Zavaleta, E. S., Eviner, V. T., Naylor, R. L., Vitousek, P. M., Reynolds, H. L., Hooper, D. U., Lavorel, S., Sala, O. E., Hobbie, S. E., Mack, M. C., & Diaz, S. (2000). Consequences of changing biodiversity. Nature, 405, 234–242.
Charcosset, J.-Y., & Chauvet, E. (2001). Effect of culture conditions on ergosterol as an indicator of biomass in the aquatic hyphomycetes. Applied and Environmental Microbiology, 67, 2051–2055.
Charcosset, J. Y., & Gardes, M. (1999). Infraspecific genetic diversity and substrate preference in the aquatic hyphomycete Tetrachaetum elegans. Mycological Research, 103, 736–742.
Chase, J. M., & Myers, J. A. (2011). Disentangling the importance of ecological niches from stochastic processes across scales. Philosophical Transactions of the Royal Society B: Biological Sciences, 366, 2351–2363.
Chauvet, E., Fabre, E., Elosegui, A., & Pozo, J. (1997). The impact of eucalypt on the leaf-associated aquatic hyphomycetes in Spanish streams. Canadian Journal of Botany-Revue Canadienne De Botanique, 75, 880–887.
Chauvet, E., & Suberkropp, K. (1998). Temperature and sporulation of aquatic hyphomycetes. Applied and Environmental Microbiology, 64, 1522–1525.
Cheever, B. M., Kratzer, E. B., & Webster, J. R. (2012). Immobilization and mineralization of N and P by heterotrophic microbes during leaf decomposition. Freshwater Science, 31, 133–147.
Cleveland, C., & Liptzin, D. (2007). C:N: P stoichiometry in soil: Is there a “Redfield ratio” for the microbial biomass? Biogeochemistry, 85, 235–252.
Cross, W. F., Benstead, J. P., Frost, P. C., & Thomas, S. A. (2005). Ecological stoichiometry in freshwater benthic systems: Recent progress and perspectives. Freshwater Biology, 50, 1895–1912.
Daam, M. A., Teixeira, H., Lillebø, A. I., & Nogueira, A. J. A. (2019). Establishing causal links between aquatic biodiversity and ecosystem functioning: Status and research needs. Science of the Total Environment, 656, 1145–1156.
Dang, C. K., Chauvet, E., & Gessner, M. O. (2005). Magnitude and variability of process rates in fungal diversity-litter decomposition relationships. Ecology Letters, 8, 1129–1137.
Dang, C. K., Schindler, M., Chauvet, E., & Gessner, M. O. (2009). Temperature oscillation coupled with fungal community shifts can modulate warming effects on litter decomposition. Ecology, 90, 122–131.
Danger, M., Cornut, J., Chauvet, E., Chavez, P., Elger, A., & Lecerf, A. (2013). Benthic algae stimulate leaf litter decomposition in detritus-based headwater streams: A case of aquatic priming effect? Ecology, 94, 1604–1613.
Danger, M., Daufresne, T., Lucas, F., Pissard, S., & Lacroix, G. (2008). Does Liebig’s law of the minimum scale up from species to communities? Oikos, 117, 1741–1751.
Danger, M., Gessner, M. O., & Bärlocher, F. (2016). Ecological stoichiometry of aquatic fungi: Current knowledge and perspectives. Fungal Ecology, 19, 100–111.
Das, M., Royer, T. V., & Leff, L. G. (2007). Diversity of fungi, bacteria, and actinomycetes on leaves decomposing in a stream. Applied and Environmental Microbiology, 73, 756–767.
Debroas, D., Domaizon, I., Humbert, J.-F., Jardillier, L., Lepère, C., Oudart, A. & Taïb, N. (2017) Overview of freshwater microbial eukaryotes diversity: A first analysis of publicly available metabarcoding data. FEMS Microbiology Ecology, 93.
Doak, D. F., Bigger, D., Harding, E. K., Marvier, M. A., O’Malley, R. E., & Thomson, D. (1998). The statistical inevitability of stability-diversity relationships in community ecology. the American Naturalist, 151, 264–276.
Duarte, S., Antunes, B., Trabulo, J., Seena, S., Cássio, F., & Pascoal, C. (2019). Intraspecific diversity affects stress response and the ecological performance of a cosmopolitan aquatic fungus. Fungal Ecology, 41, 218–223.
Duarte, S., Bärlocher, F., Cássio, F., & Pascoal, C. (2014). Current status of DNA barcoding of aquatic hyphomycetes. Sydowia, 66, 191–202.
Duarte, S., Bärlocher, F., Pascoal, C., & Cássio, F. (2016). Biogeography of aquatic hyphomycetes: Current knowledge and future perspectives. Fungal Ecology, 19, 169–181.
Duarte, S., Bärlocher, F., Trabulo, J., Cássio, F., & Pascoal, C. (2015). Stream-dwelling fungal decomposer communities along a gradient of eutrophication unraveled by 454 pyrosequencing. Fungal Diversity, 70, 127–148.
Duarte, S., Cássio, F., Ferreira, V., Canhoto, C., & Pascoal, C. (2016). Seasonal variability may affect microbial decomposers and leaf decomposition more than warming in streams. Microbial Ecology, 72, 263–276.
Duarte, S., Cássio, F., Pascoal, C., & Bärlocher, F. (2017). Taxa-area relationship of aquatic fungi on deciduous leaves. PLoS ONE, 12, e0181545.
Duarte, S., Pascoal, C., Alves, A., Correia, A., & Cássio, F. (2008). Copper and zinc mixtures induce shifts in microbial communities and reduce leaf litter decomposition in streams. Freshwater Biology, 53, 91–101.
Duarte, S., Pascoal, C., Alves, A., Correia, A., & Cássio, F. (2010). Assessing the dynamic of microbial communities during leaf decomposition in a low-order stream by microscopic and molecular techniques. Microbiological Research, 165, 351–362.
Duarte, S., Pascoal, C., Cássio, F., & Bärlocher, F. (2006). Aquatic hyphomycete diversity and identity affect leaf litter decomposition in microcosms. Oecologia, 147, 658–666.
Duarte, S., Pascoal, C., Garabetian, F., Cássio, F., & Charcosset, J.-Y. (2009). Microbial decomposer communities are mainly structured by trophic status in circumneutral and alkaline streams. Applied and Environmental Microbiology, 75, 6211–6221.
Duarte, S., Seena, S., Bärlocher, F., Pascoal, C., & Cássio, F. (2013). A decade’s perspective on the impact of DNA sequencing on aquatic hyphomycete research. Fungal Biology Reviews, 27, 19–24.
Ducklow, H. (2008). Microbial services: Challenges for microbial ecologists in a changing world. Aquatic Microbial Ecology, 53, 13–19.
Dudgeon, D., Arthington, A. H., Gessner, M. O., Kawabata, Z. I., Knowler, D. J., Leveque, C., Naiman, R. J., Prieur-Richard, A. H., Soto, D., Stiassny, M. L. J., & Sullivan, C. A. (2006). Freshwater biodiversity: Importance, threats, status and conservation challenges. Biological Reviews, 81, 163–182.
Dunck, B., Lima-Fernandes, E., Cássio, F., Cunha, A., Rodrigues, L., & Pascoal, C. (2015). Responses of primary production, leaf litter decomposition and associated communities to stream eutrophication. Environmental Pollution, 202, 32–40.
Enríquez, S., Duarte, C. M., & Sand-Jensen, K. (1993). Patterns in decomposition rates among photosynthetic organisms: The importance of detritus C:N: P content. Oecologia, 94, 457–471.
Feckler, A. & Bundschuh, M. (2020) Decoupled structure and function of leaf-associated microorganisms under anthropogenic pressure: potential hurdles for environmental monitoring. Freshwater Science, 39, 652–664.
Feckler, A., Schrimpf, A., Bundschuh, M., Bärlocher, F., Baudy, P., Cornut, J., & Schulz, R. (2017). Quantitative real-time PCR as a promising tool for the detection and quantification of leaf-associated fungal species—A proof-of-concept using Alatospora pulchella. PLoS ONE, 12, e0174634.
Fernandes, I., Duarte, S., Cássio, F., & Pascoal, C. (2013). Effects of riparian plant diversity loss on aquatic microbial decomposers become more pronounced with increasing time. Microbial Ecology, 66, 763–772.
Fernandes, I., Pascoal, C., & Cássio, F. (2011). Intraspecific traits change biodiversity effects on ecosystem functioning under metal stress. Oecologia, 166, 1019–1028.
Fernandes, I., Pascoal, C., Guimarães, H., Pinto, R., Sousa, I., & Cássio, F. (2012). Higher temperature reduces the effects of litter quality on decomposition by aquatic fungi. Freshwater Biology, 57, 2306–2317.
Fernandes, I., Pereira, A., Trabulo, J., Pascoal, C., Cássio, F., & Duarte, S. (2015). Microscopy- or DNA-based analyses: Which methodology gives a truer picture of stream-dwelling decomposer fungal diversity? Fungal Ecology, 18, 130–134.
Fernandes, I., Seena, S., Pascoal, C., & Cássio, F. (2014). Elevated temperature may intensify the positive effects of nutrients on microbial decomposition in streams. Freshwater Biology, 59, 2390–2399.
Fernandes, I., Uzun, B., Pascoal, C., & Cássio, F. (2009). Responses of aquatic fungal communities on leaf litter to temperature-change events. International Review of Hydrobiology, 94, 410–418.
Ferreira, V. (2020). Impact of climate change on aquatic hyphomycetes. Climate change and microbial ecology: current research and future trends (Ed. J. Marxsen). Norfolk, UK: Caister Academic Press.
Ferreira, V., Castagneyrol, B., Koricheva, J., Gulis, V., Chauvet, E., & Graça, M. A. S. (2015). A meta-analysis of the effects of nutrient enrichment on litter decomposition in streams. Biological Reviews, 90, 669–688.
Ferreira, V., Castela, J., Rosa, P., Tonin, A. M., Boyero, L., & Graça, M. A. S. (2016). Aquatic hyphomycetes, benthic macroinvertebrates and leaf litter decomposition in streams naturally differing in riparian vegetation. Aquatic Ecology, 50, 711–725.
Ferreira, V., & Chauvet, E. (2011a). Future increase in temperature more than decrease in litter quality can affect microbial litter decomposition in streams. Oecologia, 167, 279–291.
Ferreira, V., & Chauvet, E. (2011b). Synergistic effects of water temperature and dissolved nutrients on litter decomposition and associated fungi. Global Change Biology, 17, 551–564.
Ferreira, V., Chauvet, E., & Canhoto, C. (2015). Effects of experimental warming, litter species, and presence of macroinvertebrates on litter decomposition and associated decomposers in a temperate mountain stream. Canadian Journal of Fisheries and Aquatic Sciences, 72, 206–216.
Ferreira, V., Elosegi, A., Gulis, V., Pozo, J., & Graça, M. A. S. (2006). Eucalyptus plantations affect fungal communities associated with leaf-litter decomposition in Iberian streams. Archiv Fur Hydrobiologie, 166, 467–490.
Ferreira, V., Faustino, H., Raposeiro, P. M., & Gonçalves, V. (2017). Replacement of native forests by conifer plantations affects fungal decomposer community structure but not litter decomposition in Atlantic island streams. Forest Ecology and Management, 389, 323–330.
Ferreira, V., & Graça, M. A. S. (2006). Do invertebrate activity and current velocity affect fungal assemblage structure in leaves? International Review of Hydrobiology, 91, 1–14.
Ferreira, V., & Graça, M. A. S. (2016). Effects of whole-stream nitrogen enrichment and litter species mixing on litter decomposition and associated fungi. Limnologica, 58, 69–77.
Ferreira, V., Gulis, V., & Graça, M. A. S. (2006). Whole-stream nitrate addition affects litter decomposition and associated fungi but not invertebrates. Oecologia, 149, 718–729.
Ferreira, V., Gulis, V., Pascoal, C. & Graça, M.A.S. (2014) Stream pollution and fungi. Freshwater Fungi and Fungus-like Organisms. De Gruyter Series: Marine and Freshwater Botany (Eds., G. Jones, K. Hyde & K.-L. Pang, pp. 389–412). Berlin, Germany: De Gruyter.
Fontaine, S., & Barot, S. (2005). Size and functional diversity of microbe populations control plant persistence and long-term soil carbon accumulation. Ecology Letters, 8, 1075–1087.
Frossard, A., Gerull, L., Mutz, M., & Gessner, M. O. (2013). Litter supply as a driver of microbial activity and community structure on decomposing leaves: A test in experimental streams. Applied and Environmental Microbiology, 79, 4965.
Frossard, A., Hammes, F., & Gessner, M. O. (2016). Flow cytometric assessment of bacterial abundance in soils, sediments and sludge. Frontiers in Microbiology, 7, 903.
Frost, P. C., Benstead, J. P., Cross, W. F., Hillebrand, H., Larson, J. H., Xenopoulos, M. A., & Yoshida, T. (2006). Threshold elemental ratios of carbon and phosphorus in aquatic consumers. Ecology Letters, 9, 774–779.
Geraldes, P., Pascoal, C., & Cássio, F. (2012). Effects of increased temperature and aquatic fungal diversity on litter decomposition. Fungal Ecology, 5, 734–740.
Gessner, M. O., & Chauvet, E. (1993). Ergosterol-to-biomass conversion factors for aquatic hyphomycetes. Applied and Environmental Microbiology, 59, 502–507.
Gessner, M. O., & Chauvet, E. (1994). Importance of stream microfungi in controlling breakdown rates of leaf-litter. Ecology, 75, 1807–1817.
Gessner, M. O., & Chauvet, E. (1997). Growth and production of aquatic hyphomycetes in decomposing leaf litter. Limnology and Oceanography, 42, 496–505.
Gessner, M. O., & Newell, S. Y. (2002). Biomass, growth rate, and production of filamentous fungi in plant litter. In H. J. Christon (Ed.), Manual of environmental microbiology. (pp. 390–408). ASM Press.
Ginzinger, D. G. (2002). Gene quantification using real-time quantitative PCR: An emerging technology hits the mainstream. Experimental Hematology, 30, 503–512.
Gonçalves, A. L., Gama, A. M., Ferreira, V., Graça, M. A. S., & Canhoto, C. (2007). The breakdown of blue gum (Eucalyptus globulus Labill.) bark in a portuguese stream. Fundamental and Applied Limnology / Archiv Für Hydrobiologie, 168, 307–315
Gonçalves, A. L., Graça, M. A. S., & Canhoto, C. (2013). The effect of temperature on leaf decomposition and diversity of associated aquatic hyphomycetes depends on the substrate. Fungal Ecology, 6, 546–553.
Gossiaux, A., Jabiol, J., Poupin, P., Chauvet, E., & Guérold, F. (2019). Seasonal variations overwhelm temperature effects on microbial processes in headwater streams: Insights from a temperate thermal spring. Aquatic Sciences, 81, 30.
Graça, M. A. S., & Abelho, M. (2020). Respiration of litter-associated microbes and invertebrates. In F. Bärlocher, M. O. Gessner, & M. A. S. Graça (Eds.), Methods to study litter decomposition (pp. 301–308). Springer.
Guenet, B., Danger, M., Abbadie, L., & Lacroix, G. (2010). Priming effect: Bridging the gap between terrestrial and aquatic ecology. Ecology, 91, 2850–2861.
Gulis, V. (2001). Are there any substrate preferences in aquatic hyphomycetes? Mycological Research, 105, 1088–1093.
Gulis, V., Ferreira, V., & Graça, M. A. S. (2006). Stimulation of leaf litter decomposition and associated fungi and invertebrates by moderate eutrophication: Implications for stream assessment. Freshwater Biology, 51, 1655–1669.
Gulis, V., Kuehn, K. A., Schoettle, L. N., Leach, D., Benstead, J. P., & Rosemond, A. D. (2017). Changes in nutrient stoichiometry, elemental homeostasis and growth rate of aquatic litter-associated fungi in response to inorganic nutrient supply. The ISME Journal, 11, 2729–2739.
Gulis, V., Marvanová, L., & Descals, E. (2020). An illustrated key to the common temperate species of aquatic hyphomycetes. In F. Bärlocher, M. O. Gessner, & M. A. S. Graça (Eds.), Methods to study litter decomposition (pp. 223–239). Springer.
Gulis, V., Su, R. & Kuehn, K.A. (2019). Fungal decomposers in freshwater environments. The structure and function of aquatic microbial communities. Advances in Environmental Microbiology (Ed., C. Hurst, pp. 121–155). Cham: Springer.
Gulis, V., & Suberkropp, K. (2003). Leaf litter decomposition and microbial activity in nutrient-enriched and unaltered reaches of a headwater stream. Freshwater Biology, 48, 123–134.
Gulis, V., & Suberkropp, K. (2004). Effects of whole-stream nutrient enrichment on the concentration and abundance of aquatic hyphomycete conidia in transport. Mycologia, 96, 57–65.
Güsewell, S., & Gessner, M. O. (2009). N : P ratios influence litter decomposition and colonization by fungi and bacteria in microcosms. Functional Ecology, 23, 211–219.
Halvorson, H. M., Francoeur, S. N., Findlay, R. H., & Kuehn, K. A. (2019). Algal-mediated priming effects on the ecological stoichiometry of leaf litter decomposition: A meta-analysis. Frontiers in Earth Science, 7, 76.
Hayer, M., Schwartz, E., Marks, J. C., Koch, B. J., Morrissey, E. M., Schuettenberg, A. A., & Hungate, B. A. (2016). Identification of growing bacteria during litter decomposition in freshwater through quantitative stable isotope probing. Environmental Microbiology Reports, 8, 975–982.
Hieber, M., & Gessner, M. O. (2002). Contribution of stream detrivores, fungi, and bacteria to leaf breakdown based on biomass estimates. Ecology, 83, 1026–1038.
Hladyz, S., Gessner, M. O., Giller, P. S., Pozo, J., & Woodward, G. (2009). Resource quality and stoichiometric constraints on stream ecosystem functioning. Freshwater Biology, 54, 957–970.
Hofstetter, V., Buyck, B., Eyssartier, G., Schnee, S., & Gindro, K. (2019). The unbearable lightness of sequenced-based identification. Fungal Diversity, 96, 243–284.
Hooper, D. U., Adair, E. C., Cardinale, B. J., Byrnes, J. E. K., Hungate, B. A., Matulich, K. L., Gonzalez, A., Duffy, J. E., Gamfeldt, L., & O’Connor, M. I. (2012). A global synthesis reveals biodiversity loss as a major driver of ecosystem change. Nature, 486, 105–108.
Hungate, B. A., Mau, R. L., Schwartz, E., Caporaso, J. G., Dijkstra, P., van Gestel, N., Koch, B. J., Liu, C. M., McHugh, T. A., Marks, J. C., Morrissey, E. M., & Price, L. B. (2015). Quantitative microbial ecology through stable isotope probing. Applied and Environmental Microbiology, 81, 7570–7581.
IPCC. (2014). Climate change 2014: Synthesis report. Contribution of working groups I, II and III to the fifth assessment report of the Intergovernmental Panel on Climate Change (Eds., Core Writing Team, R.K. Pachauri & L.A. Meyer). Geneva, Switzerland: IPCC.
Jabiol, J., Lecerf, A., Lamothe, S., Gessner, M. O., & Chauvet, E. (2019). Litter quality modulates effects of dissolved nitrogen on leaf decomposition by stream microbial communities. Microbial Ecology, 77, 959–966.
Kanagawa, T. (2003). Bias and artifacts in multitemplate polymerase chain reactions (PCR). Journal of Bioscience and Bioengineering, 96, 317–323.
Keiblinger, K. M., Hall, E. K., Wanek, W., Szukics, U., Hämmerle, I., Ellersdorfer, G., Böck, S., Strauss, J., Sterflinger, K., Richter, A., & Zechmeister-Boltenstern, S. (2010). The effect of resource quantity and resource stoichiometry on microbial carbon-use-efficiency. FEMS Microbiology Ecology, 73, 430–440.
Komínková, D., Kuehn, K. A., Büsing, N., Steiner, D., & Gessner, M. O. (2000). Microbial biomass, growth, and respiration associated with submerged litter of Phragmites australis decomposing in a littoral reed stand of a large lake. Aquatic Microbial Ecology, 22, 271–282.
Kuehn, K. A., Francoeur, S. N., Findlay, R. H., & Neely, R. K. (2014). Priming in the microbial landscape: Periphytic algal stimulation of litter-associated microbial decomposers. Ecology, 95, 749–762.
Laitung, B., & Chauvet, E. (2005). Vegetation diversity increases species richness of leaf-decaying fungal communities in woodland streams. Archiv Fur Hydrobiologie, 164, 217–235.
Laitung, B., Chauvet, E., Feau, N., Feve, K., Chikhi, L., & Gardes, M. (2004). Genetic diversity in Tetrachaetum elegans, a mitosporic aquatic fungus. Molecular Ecology, 13, 1679–1692.
Laitung, B., Pretty, J. L., Chauvet, E., & Dobson, M. (2002). Response of aquatic hyphomycete communities to enhanced stream retention in areas impacted by commercial forestry. Freshwater Biology, 47, 313–323.
Lecerf, A., Dobson, M., Dang, C. K., & Chauvet, E. (2005). Riparian plant species loss alters trophic dynamics in detritus-based stream ecosystems. Oecologia, 146, 432–442.
Lecerf, A., Marie, G., Kominoski, J. S., LeRoy, C. J., Bernadet, C., & Swan, C. M. (2011). Incubation time, functional litter diversity, and habitat characteristics predict litter-mixing effects on decomposition. Ecology, 92, 160–169.
Letourneau, A., Seena, S., Marvanová, L., & Bärlocher, F. (2010). Potential use of barcoding to identify aquatic hyphomycetes. Fungal Diversity, 40, 51–64.
Lima-Fernandes, E., Fernandes, I., Geraldes, P., Pereira, A., Cássio, F., & Pascoal, C. (2015). Eutrophication modulates plant-litter diversity effects on litter decomposition in streams. Freshwater Science, 34, 31–41.
Loreau, M., & Hector, A. (2001). Partitioning selection and complementarity in biodiversity experiments. Nature, 412, 72–76.
Manerkar, M. A., Seena, S., & Bärlocher, F. (2008). Q-RT-PCR for assessing archaea, bacteria, and fungi during leaf decomposition in a stream. Microbial Ecology, 56, 467–473.
Manzoni, S., Trofymow, J. A., Jackson, R. B., & Porporato, A. (2010). Stoichiometric controls on carbon, nitrogen, and phosphorus dynamics in decomposing litter. Ecological Monographs, 80, 89–106.
Martínez, A., Larrañaga, A., Pérez, J., Descals, E., Basaguren, A., & Pozo, J. (2013). Effects of pine plantations on structural and functional attributes of forested streams. Forest Ecology and Management, 310, 147–155.
McArthur, F. A., Baerlocher, M. O., MacLean, N. A. B., Hiltz, M. D., & Bärlocher, F. (2001). Asking probing questions: Can fluorescent in situ hybridization identify and localise aquatic hyphomycetes on leaf litter? International Review of Hydrobiology, 86, 429–438.
Medeiros, A. O., Pascoal, C., & Graça, M. A. S. (2009). Diversity and activity of aquatic fungi under low oxygen conditions. Freshwater Biology, 54, 142–149.
Melillo, J. M., Aber, J. D., & Muratore, J. F. (1982). Nitrogen and lignin control of hardwood leaf litter decomposition dynamics. Ecology, 63, 621–626.
Mille-Lindblom, C., von Wachenfeldt, E., & Tranvik, L. J. (2004). Ergosterol as a measure of living fungal biomass: Persistence in environmental samples after fungal death. Journal of Microbiological Methods, 59, 253–262.
Mooshammer, M., Wanek, W., Zechmeister-Boltenstern, S., & Richter, A. (2014). Stoichiometric imbalances between terrestrial decomposer communities and their resources: Mechanisms and implications of microbial adaptations to their resources. Frontiers in Microbiology, 5, 22–22.
Mora-Gómez, J., Boix, D., Duarte, S., Cássio, F., Pascoal, C., Elosegi, A., & Romaní, A. M. (2020). Legacy of summer drought on autumnal leaf litter processing in a temporary mediterranean stream. Ecosystems, 23, 989–1003.
Nikolcheva, L. G., & Bärlocher, F. (2002). Phylogeny of Tetracladium based on 18S rDNA. Czech Mycology, 53, 285–295.
Nikolcheva, L. G., & Bärlocher, F. (2004). Taxon-specific fungal primers reveal unexpectedly high diversity during leaf decomposition in a stream. Mycological Progress, 3, 41–49.
Nikolcheva, L. G., & Bärlocher, F. (2005). Seasonal and substrate preferences of fungi colonizing leaves in streams: Traditional versus molecular evidence. Environmental Microbiology, 7, 270–280.
Nikolcheva, L. G., Cockshutt, A. M., & Bärlocher, F. (2003). Determining diversity of freshwater fungi on decaying leaves: Comparison of traditional and molecular approaches. Applied and Environmental Microbiology, 69, 2548–2554.
Pascoal, C., & Cássio, F. (2004). Contribution of fungi and bacteria to leaf litter decomposition in a polluted river. Applied and Environmental Microbiology, 70, 5266–5273.
Pascoal, C., & Cássio, F. (2008). Linking fungal diversity to the functioning of freshwater ecosystems. In K. R. Sridhar, F. Bärlocher, & K. D. Hyde (Eds.), Novel techniques and ideas in mycology (pp. 1–15). Fungal Diversity Press.
Pascoal, C., Cássio, F., Marcotegui, A., Sanz, B., & Gomes, P. (2005). Role of fungi, bacteria, and invertebrates in leaf litter breakdown in a polluted river. Journal of the North American Benthological Society, 24, 784–797.
Pascoal, C., Cássio, F., Nikolcheva, L., & Bärlocher, F. (2010). Realized fungal diversity increases functional stability of leaf litter decomposition under zinc stress. Microbial Ecology, 59, 84–93.
Pascoal, C., Marvanová, L., & Cássio, F. (2005). Aquatic hyphomycete diversity in streams of Northwest Portugal. Fungal Diversity, 19, 109–128.
Peláez, F., Platas, G., Collado, J., & Díez, M. T. (1996). Infraspecific variation in two species of aquatic hyphomycetes assessed by RAPD analysis. Mycological Research, 100, 831–837.
Pereira, A., Geraldes, P., Lima-Fernandes, E., Fernandes, I., Cássio, F., & Pascoal, C. (2016). Structural and functional measures of leaf-associated invertebrates and fungi as predictors of stream eutrophication. Ecological Indicators, 69, 648–656.
Pérez, J., Galán, J., Descals, E., & Pozo, J. (2014). Effects of fungal inocula and habitat conditions on alder and eucalyptus leaf litter decomposition in streams of Northern Spain. Microbial Ecology, 67, 245–255.
Pimentão, A. R., Pascoal, C., Castro, B. B., & Cássio, F. (2020). Fungistatic effect of agrochemical and pharmaceutical fungicides on non-target aquatic decomposers does not translate into decreased fungi- or invertebrate-mediated decomposition. Science of the Total Environment, 712, 135676.
Pope, C. A., Halvorson, H. M., Findlay, R. H., Francoeur, S. N., & Kuehn, K. A. (2020). Light and temperature mediate algal stimulation of heterotrophic activity on decomposing leaf litter. Freshwater Biology, 65, 1210–1222.
Pradhan, A., Seena, S., Pascoal, C., & Cássio, F. (2011). Can metal nanoparticles be a threat to microbial decomposers of plant litter in streams? Microbial Ecology, 62, 58–68.
Rajashekhar, M., & Kaveriappa, K. M. (2003). Diversity of aquatic hyphomycetes in the aquatic ecosystems of the Western Ghats of India. Hydrobiologia, 501, 167–177.
Raviraja, N. S., Nikolcheva, L. G., & Barlocher, F. (2006). Fungal growth and leaf decomposition are affected by amount and type of inoculum and by external nutrients. Sydowia, 58, 91–104.
Rico, A., Dimitrov, M. R., Van Wijngaarden, R. P. A., Satapornvanit, K., Smidt, H., & Van den Brink, P. J. (2014). Effects of the antibiotic enrofloxacin on the ecology of tropical eutrophic freshwater microcosms. Aquatic Toxicology, 147, 92–104.
Romaní, A. M., Fischer, H., Mille-Lindblom, C., & Tranvik, L. J. (2006). Interactions of bacteria and fungi on decomposing litter: Differential extracellular enzyme activities. Ecology, 87, 2559–2569.
Rosemond, A. D., Benstead, J. P., Bumpers, P. M., Gulis, V., Kominoski, J. S., Manning, D. W. P., Suberkropp, K., & Wallace, J. B. (2015). Experimental nutrient additions accelerate terrestrial carbon loss from stream ecosystems. Science, 347, 1142–1145.
Sales, M. A., Gonçalves, J. F., Dahora, J. S., & Medeiros, A. O. (2015). Influence of leaf quality in microbial decomposition in a headwater stream in the Brazilian Cerrado: A 1-year study. Microbial Ecology, 69, 84–94.
Sampaio, A., Cortes, R., & Leão, C. (2004). Yeast and macroinvertebrate communities associated with leaf litter decomposition in a second order stream. International Review of Hydrobiology, 89, 453–466.
Sampaio, A., Sampaio, J. P., & Leão, C. (2007). Dynamics of yeast populations recovered from decaying leaves in a nonpolluted stream: A 2-year study on the effects of leaf litter type and decomposition time. FEMS Yeast Research, 7, 595–603.
Sardans, J., Rivas-Ubach, A., & Peñuelas, J. (2012). The elemental stoichiometry of aquatic and terrestrial ecosystems and its relationships with organismic lifestyle and ecosystem structure and function: A review and perspectives. Biogeochemistry, 111, 1–39.
Schloss, P.D., Girard, R.A., Martin, T., Edwards, J. & Thrash, J.C. (2016) Status of the archaeal and bacterial census: an update. mBio, 7, e00201–00216.
Seena, S., Bärlocher, F., Sobral, O., Gessner, M. O., Dudgeon, D., McKie, B. G., Chauvet, E., Boyero, L., Ferreira, V., Frainer, A., Bruder, A., Matthaei, C. D., Fenoglio, S., Sridhar, K. R., Albariño, R. J., Douglas, M. M., Encalada, A. C., Garcia, E., Ghate, S. D., … Graça, M. A. S. (2019). Biodiversity of leaf litter fungi in streams along a latitudinal gradient. Science of the Total Environment, 661, 306–315.
Seena, S., Duarte, S., Pascoal, C., & Cássio, F. (2012). Intraspecific variation of the aquatic fungus Articulospora tetracladia: An ubiquitous perspective. PLoS ONE, 7, e35884.
Seena, S., Graça, D., Bartels, A., & Cornut, J. (2019). Does nanosized plastic affect aquatic fungal litter decomposition? Fungal Ecology, 39, 388–392.
Seena, S., Marvanová, L., Letourneau, A., & Bärlocher, F. (2018). Articulospora – Phylogeny vs morphology. Fungal Biology, 122, 965–976.
Seena, S., & Monroy, S. (2016). Preliminary insights into the evolutionary relationships of aquatic hyphomycetes and endophytic fungi. Fungal Ecology, 19, 128–134.
Seena, S., Pascoal, C., Marvanova, L., & Cassio, F. (2010). DNA barcoding of fungi: A case study using ITS sequences for identifying aquatic hyphomycete species. Fungal Diversity, 44, 77–87.
Seena, S., Sobral, O., & Cano, A. (2020). Metabolomic, functional, and ecologic responses of the common freshwater fungus Neonectria lugdunensis to mine drainage stress. Science of the Total Environment, 718, 137359.
Seena, S., Wynberg, N., & Bärlocher, F. (2008). Fungal diversity during leaf decomposition in a stream assessed through clone libraries. Fungal Diversity, 30, 1–14.
Sinsabaugh, R. L., & Follstad Shah, J. J. (2011). Ecoenzymatic stoichiometry of recalcitrant organic matter decomposition: The growth rate hypothesis in reverse. Biogeochemistry, 102, 31–43.
Sinsabaugh, R. L., Manzoni, S., Moorhead, D. L., & Richter, A. (2013). Carbon use efficiency of microbial communities: Stoichiometry, methodology and modelling. Ecology Letters, 16, 930–939.
Solé, M., Fetzer, I., Wennrich, R., Sridhar, K. R., Harms, H., & Krauss, G. (2008). Aquatic hyphomycete communities as potential bioindicators for assessing anthropogenic stress. Science of the Total Environment, 389, 557–565.
Sridhar, K. R., & Bärlocher, F. (1994). Viability of aquatic hyphomycete conidia in foam. Canadian Journal of Botany, 72, 106–110.
Sridhar, K. R., & Bärlocher, F. (2011). Reproduction of aquatic hyphomycetes at low concentrations of Ca2+, Zn2+, Cu2+, and Cd2+. Environmental Toxicology and Chemistry, 30, 2868–2873.
Sridhar, K. R., Duarte, S., Cássio, F., & Pascoal, C. (2009). The role of early fungal colonizers in leaf-litter decomposition in Portuguese streams impacted by agricultural runoff. International Review of Hydrobiology, 94, 399–409.
Stegen, J. C., Lin, X., Konopka, A. E., & Fredrickson, J. K. (2012). Stochastic and deterministic assembly processes in subsurface microbial communities. The ISME Journal, 6, 1653–1664.
Stelzer, R. S., Heffernan, J., & Likens, G. E. (2003). The influence of dissolved nutrients and particulate organic matter quality on microbial respiration and biomass in a forest stream. Freshwater Biology, 48, 1925–1937.
Sterner, R. W., & Elser, J. J. (2002). Stochiometry and Homeostasis. In R. W. Sterner & J. J. Elser (Eds.), Ecological Stoichiometry: The Biology of Elements from Molecules to the Biosphere. (pp. 2–43). Princeton University Press.
Suberkropp, K. (1984). Effect of temperature on seasonal occurrence of aquatic hyphomycetes. Transactions of the British Mycological Society, 82, 53–62.
Suberkropp, K. (1991). Relationships between growth and sporulation of aquatic hyphomycetes on decomposing leaf litter. Mycological Research, 95, 843–850.
Suberkropp, K., Gessner, M. O., & Kuehn, K. A. (2020). Fungal growth rates and production. In F. Bärlocher, M. O. Gessner, & M. A. S. Graça (Eds.), Methods to study litter decomposition. (pp. 257–264). Springer.
Suberkropp, K., Godshalk, G. L., & Klug, M. J. (1976). Changes in the chemical composition of leaves during processing in a woodland stream. Ecology, 57, 720–727.
Suberkropp, K., & Klug, M. J. (1976). Fungi and bacteria associated with leaves during processing in a woodland stream. Ecology, 57, 707–719.
Tlili, A., Berard, A., Blanck, H., Bouchez, A., Cássio, F., Eriksson, K. M., Morin, S., Montuelle, B., Navarro, E., Pascoal, C., Pesce, S., Schmitt-Jansen, M., & Behra, R. (2016). Pollution-induced community tolerance (PICT): Towards an ecologically relevant risk assessment of chemicals in aquatic systems. Freshwater Biology, 61, 2141–2151.
Tlili, A., Jabiol, J., Behra, R., Gil-Allué, C., & Gessner, M. O. (2017). Chronic exposure effects of silver nanoparticles on stream microbial decomposer communities and ecosystem functions. Environmental Science & Technology, 51, 2447–2455.
Treton, C., Chauvet, E., & Charcosset, J.-Y. (2004). Competitive interaction between two aquatic hyphomycete species and increase in leaf litter breakdown. Microbial Ecology, 48, 439–446.
Vellend, B. M. (2010). Conceptual synthesis in community ecology. The Quarterly Review of Biology, 85, 183–206.
Woodward, G., Gessner, M. O., Giller, P. S., Gulis, V., Hladyz, S., Lecerf, A., Malmqvist, B., McKie, B. G., Tiegs, S. D., Cariss, H., Dobson, M., Elosegi, A., Ferreira, V., Graça, M. A. S., Fleituch, T., Lacoursière, J. O., Nistorescu, M., Pozo, J., Risnoveanu, G., … Chauvet, E. (2012). Continental-scale effects of nutrient pollution on stream ecosystem functioning. Science, 336, 1438–1440.
Wurzbacher, C., Grimmett, I. J. & Bärlocher, F. (2015) Metabarcoding-based fungal diversity on coarse and fine particulate organic matter in a first-order stream in Nova Scotia, Canada. F1000Research, 4, 1378–1378.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Pascoal, C., Fernandes, I., Seena, S., Danger, M., Ferreira, V., Cássio, F. (2021). Linking Microbial Decomposer Diversity to Plant Litter Decomposition and Associated Processes in Streams. In: Swan, C.M., Boyero, L., Canhoto, C. (eds) The Ecology of Plant Litter Decomposition in Stream Ecosystems. Springer, Cham. https://doi.org/10.1007/978-3-030-72854-0_9
Download citation
DOI: https://doi.org/10.1007/978-3-030-72854-0_9
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-72853-3
Online ISBN: 978-3-030-72854-0
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)