Skip to main content
SpringerLink
Log in
Book cover

Mudflat Ecology pp 43–61Cite as

Microbiota: The Living Foundation

  • Chapter
  • First Online:

Part of the book series: Aquatic Ecology Series ((AQEC,volume 7))

Abstract

Mudflats are highly productive regions that are important to local, regional and global aspects of ecology and biogeochemistry. They sequester organic carbon, recycle nutrient elements such as nitrogen and phosphorus, release climate-active gases to the atmosphere, and provide sustenance to countless resident and migrant animals. Microorganisms that remain hidden from sight underpin all of these, and many other, crucial ecosystem functions and services. This chapter explores the roles of microorganisms in mudflat sediments, their interactions with the other residents, and some of the contemporary techniques used to study and quantify the ways in which they influence biogeochemical cycles.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD   199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  • Allison SD, Martiny JBH (2008) Colloquium paper: resistance, resilience, and redundancy in microbial communities. Proc Natl Acad Sci USA 105:11512–11519

    Article  CAS  PubMed  Google Scholar 

  • Anderson NH, Sedell JR (1979) Detritus processing by macroinvertebrates in stream ecosystems. Annu Rev Entomol 24:351–377

    Article  Google Scholar 

  • Anderson TR, Pond DW, Mayor DJ (2017) The role of microbes in the nutrition of detritivorous invertebrates: a stoichiometric analysis. Front Microbiol 7:1–13

    Article  Google Scholar 

  • Arnosti C (2004) Speed bumps and barricades in the carbon cycle: substrate structural effects on carbon cycling. Mar Chem 92:263–273

    Article  CAS  Google Scholar 

  • Arnosti C, Jørgensen BB, Sageman J, Thamdrup B (1998) Temperature dependence of microbial degradation of organic matter in marine sediments: polysaccharide hydrolysis, oxygen consumption, and sulfate reduction. Mar Ecol Prog Ser 165:59–70

    Article  CAS  Google Scholar 

  • Austin HK, Findlay SE (1989) Benthic bacterial biomass and production in the Hudson River estuary. Microb Ecol 18:105–116

    Article  CAS  PubMed  Google Scholar 

  • Azam F, Fenchel T, Field J, Gray J, Meyer-Reil L, Thingstad F (1983) The ecological role of water-column microbes in the Sea. Mar Ecol Prog Ser 10:257–263

    Article  Google Scholar 

  • Baier CR (1935) Studien zur hydrobakteriologie stehender binnengewasser. Arch Hydrobiol 29:183–264

    Google Scholar 

  • Bange HW, Bartell UH, Rapsomanikis S, Andreae MO (1994) Computed with two different exchange models lie in the range of 11-18 Tg CH TM (phosphorus). North 8:465–480

    CAS  Google Scholar 

  • Bartels P, Cucherousset J, Steger K, Eklov P, Tranvik LJ, Hillebrand H (2012) Reciprocal subsidies between freshwater and terrestrial ecosystems structure consumer resource dynamics. Ecology 93:1173–1182

    Article  PubMed  Google Scholar 

  • Bertics VJ, Ziebis W (2009) Biodiversity of benthic microbial communities in bioturbated coastal sediments is controlled by geochemical microniches. ISME J 3:1269–1285

    Article  CAS  PubMed  Google Scholar 

  • Bertics VJ, Ziebis W (2010) Bioturbation and the role of microniches for sulfate reduction in coastal marine sediments. Environ Microbiol 12:3022–3034

    Article  CAS  PubMed  Google Scholar 

  • Bianchi TS (2011) The role of terrestrially derived organic carbon in the coastal ocean: a changing paradigm and the priming effect. Proc Natl Acad Sci USA 108:19473–19481

    Article  CAS  PubMed  Google Scholar 

  • Bingemann CW, Varner JE, Martin WP (1953) The effect of the addition of organic materials on the decomposition of an organic soil. Soil Sci Soc Am J 17:34–38

    Article  Google Scholar 

  • Bonaglia S, Nascimento FJA, Bartoli M, Klawonn I, Brüchert V (2014) Meiofauna increases bacterial denitrification in marine sediments. Nat Commun 5:5133

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Boschker HTS, Nold SC, Wellsbury P, Bos D, de Graaf W, Pel R, Parkes RJ, Cappenberg TE (1998) Direct linking of microbial populations to specific biogeochemical processes by 13C-labelling of biomarkers. Nature 392:396–400

    Article  Google Scholar 

  • Boschker HTS, de Brouwer JFC, Cappenberg TE (1999) The contribution of macrophyte-derived organic matter to microbial biomass in salt-marsh sediments: stable carbon isotope analysis of microbial biomarkers. Limnol Oceanogr 44:309–319

    Article  Google Scholar 

  • Bouillon S, Boschker HTS (2006) Bacterial carbon sources in coastal sediments: a cross-system analysis based on stable isotope data of biomarkers. Biogeosciences 3:175–185

    Article  CAS  Google Scholar 

  • Broadbent FE (1947) Nitrogen release and carbon loss from soil organic matter during decomposition of added plant residues. Soil Sci Soc Am Proc 12:246–249

    Article  Google Scholar 

  • Burdige DJ (2007) Preservation of organic matter in marine sediments: controls, mechanisms, and an imbalance in sediment organic carbon budgets? Chem Rev 107:467–485

    Article  CAS  PubMed  Google Scholar 

  • Cai W-J (2011) Estuarine and coastal ocean carbon paradox: CO2 sinks or sites of terrestrial carbon incineration? Annu Rev Mar Sci 3:123–145

    Article  Google Scholar 

  • Carpenter SR (1996) Microcosm experiments have limited relevance for community and ecosystem ecology. Ecology 77:677–680

    Article  Google Scholar 

  • Cebrián J, Duarte CM (1995) Plant growth-rate dependence of detrital carbon storage in ecosystems. Science (New York, N.Y.) 268:1606–1608

    Article  Google Scholar 

  • Chen X, Andersen TJ, Morono Y, Inagaki F, Jørgensen BB, Lever MA (2017) Bioturbation as a key driver behind the dominance of bacteria over archaea in near-surface sediment. Sci Rep 7:1–14

    Article  CAS  Google Scholar 

  • Cole JJ, Prairie YT, Caraco NF, McDowell WH, Tranvik LJ, Striegl RG, Duarte CM, Kortelainen P, Downing JA, Middelburg JJ, Melack J (2007) Plumbing the global carbon cycle: integrating inland waters into the terrestrial carbon budget. Ecosystems 10:171–184

    Article  CAS  Google Scholar 

  • Cook PLM, Revill AT, Butler ECV, Eyre BD (2004) Carbon and nitrogen cycling on intertidal mudflats of a temperate Australian estuary. II. Nitrogen cycling. Mar Ecol Prog Ser 280:39–54

    Article  CAS  Google Scholar 

  • Cook PLM, Veuger B, Böer S, Middelburg JJ (2007) Effect of nutrient availability on carbon and nitrogen incorporation and flows through benthic algae and bacteria in near-shore sandy sediment. Aquat Microb Ecol 49:165–180

    Article  Google Scholar 

  • Coplen TB (1996) New guidelines for reporting stable hydrogen, carbon, and oxygen isotope-ratio data. Geochim Cosmochim Acta 60:3359–3360

    Article  CAS  Google Scholar 

  • Currie AR, Tait K, Parry H, de Francisco-Mora B, Hicks N, Mark Osborn A, Widdicombe S, Stahl H (2017) Marine microbial gene abundance and community composition in response to ocean acidification and elevated temperature in two contrasting coastal marine sediments. Front Microbiol 8:1599

    Article  PubMed  PubMed Central  Google Scholar 

  • Danovaro R (2000) Benthic microbial loop and meiofaunal response to oil-induced disturbance in coastal sediments: a review. Int J Environ Pollut 13:380

    Article  CAS  Google Scholar 

  • Del Giorgio PA, Cole JJ (1998) Bacterial growth efficiency in natural aquatic systems. Annu Rev Ecol Syst 29:503–554

    Article  Google Scholar 

  • Duyl FCV, Kop AJ (1990) Seasonal patterns of bacterial production and biomass in intertidal sediments of the western Dutch Wadden Sea. Mar Ecol Prog Ser 59:249–261

    Article  Google Scholar 

  • Engel A, Händel N, Wohlers J, Lunau M, Grossart HP, Sommer U, Riebesell U (2011) Effects of sea surface warming on the production and composition of dissolved organic matter during phytoplankton blooms: results from a mesocosm study. J Plankton Res 33:357–372

    Article  CAS  Google Scholar 

  • Epstein SS (1997) Microbial food webs in marine sediments. I. Trophic interactions and grazing rates in two tidal flat communities. Microb Ecol 34:188–198

    Article  CAS  PubMed  Google Scholar 

  • Evrard V, Huettel M, Cook PLM, Soetaert K, Heip CHR, Middelburg JJ (2012) Importance of phytodetritus and microphyto benthos for heterotrophs in a shallow subtidal sandy sediment. Mar Ecol Prog Ser 455:13–31

    Article  CAS  Google Scholar 

  • Falkowski PG, Fenchel T, DeLong EF (2008) The microbial engines that drive earth’s biogeochemical cycles. Science 320:1034–1039

    Article  CAS  PubMed  Google Scholar 

  • Farquhar GD, Ehleringer JR, Hubick KT (1989) Carbon isotope discrimination and photosynthesis. Annu Rev Plant Physiol Plant Mol Biol 40:503–537

    Article  CAS  Google Scholar 

  • Fenchel T (1970) Studies on the decomposition of organic detritus derived from the turtle grass Thalassia testudinum. Limnol Oceanogr 15:14–20

    Article  Google Scholar 

  • Fenchel T (2008) The microbial loop - 25 years later. J Exp Mar Biol Ecol 366:99–103

    Article  Google Scholar 

  • Fenchel T, Jørgensen BB (1977) Detritus food chains of aquatic ecosystems: the role of bacteria. Adv Microb Ecol 1:1–58

    Article  CAS  Google Scholar 

  • France RL (2011) Leaves as “crackers”, biofilm as “peanut butter”: exploratory use of stable isotopes as evidence for microbial pathways in detrital food webs. Oceanol Hydrobiol Stud 40:110–115

    Article  Google Scholar 

  • Frankignoulle M, Abril G, Borges A, Bourge I, Canon C, Delille B, Libert E, Théate JM (1998) Carbon dioxide emission from European estuaries. Science 282:434–436

    Article  CAS  PubMed  Google Scholar 

  • Frostegård Å, Bååth E, Tunlid A (1993) Shifts in the structure of soil microbial communities in limed forests as revealed by phospholipid fatty acid analysis. Soil Biol Biochem 25:723–730

    Article  Google Scholar 

  • Frostegård Å, Tunlid A, Bååth E (2011) Use and misuse of PLFA measurements in soils. Soil Biol Biochem 43:1621–1625

    Article  CAS  Google Scholar 

  • Fry B (2006) Stable isotope ecology. Springer, Berlin

    Book  Google Scholar 

  • Gilbertson WW, Solan M, Prosser JI (2012) Differential effects of microorganism-invertebrate interactions on benthic nitrogen cycling. FEMS Microbiol Ecol 82:11–22

    Article  PubMed  Google Scholar 

  • Glud RN (2008) Oxygen dynamics of marine sediments. Mar Biol Res 4:243–228

    Article  Google Scholar 

  • Godbold JA, Solan M (2013) Long-term effects of warming and ocean acidification are modified by seasonal variation in species responses and environmental conditions. Philos Trans R Soc 368:20130186

    Article  CAS  Google Scholar 

  • Godbold JA, Hale R, Wood CL, Solan M (2017) Vulnerability of macronutrients to the concurrent effects of enhanced temperature and atmospheric pCO2 in representative shelf sea sediment habitats. Biogeochemistry 135:89–10

    Article  CAS  Google Scholar 

  • Gontikaki E, Mayor DJ, Thornton B, Black K, Witte U (2011) Processing of 13C-labelled diatoms by a bathyal community at sub-zero temperatures. Mar Ecol Prog Ser 421:39–50

    Article  CAS  Google Scholar 

  • Goto N, Mitamura O, Terai H (2001) Biodegradation of photosynthetically produced extracellular organic carbon from intertidal benthic algae. J Exp Mar Biol Ecol 257:73–86

    Article  CAS  PubMed  Google Scholar 

  • Guckert JB, Antworth CP, Nichols PD, White DC (1985) Phospholipid, ester-linked fatty acid profiles as reproducible assays for changes in prokaryotic community structure of estuarine sediments. FEMS Microbiol Lett 31:147–158

    Article  CAS  Google Scholar 

  • Guckert JB, Hood MA, White DC (1986) Phospholipid ester-linked fatty acid profile changes during nutrient deprivation of Vibrio cholerae: increases in the trans/cis ratio and proportions of cyclopropyl fatty acids. Appl Environ Microbiol 52:794–801

    CAS  PubMed  PubMed Central  Google Scholar 

  • Guckert JB, Ringelberg DB, White DC, Hanson RS, Bratina BJ (1991) Membrane fatty acids as phenotypic markers in the polyphasic taxonomy of methylotrophs within the Proteobacteria. J Gen Microbiol 137:2631–2641

    Article  CAS  PubMed  Google Scholar 

  • Guenet B, Danger M, Abbadie L, Lacroix G (2010) Priming effect: bridging the gap between terrestrial and aquatic ecology. Ecology 91:2850–2861

    Article  PubMed  Google Scholar 

  • Guenet B, Camino-Serrano M, Ciais P, Tifafi M, Maignan F, Soong JL, Janssens IA (2018) Impact of priming on global soil carbon stocks. Glob Change Biol:1–11

    Google Scholar 

  • Harrison PG, Mann KH (1975) Detritus formation from eelgrass (Zostera marina L.): the relative effects of fragmentation, leaching, and decay. Limnol Oceanogr 20:924–934

    Article  CAS  Google Scholar 

  • Haynes K, Hofmann TA, Smith CJ, Ball AS, Underwood GJC, Osborn AM (2007) Diatom-derived carbohydrates as factors affecting bacterial community composition in estuarine sediments. Appl Environ Microbiol 73:6112–6124

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Heip CHR, Goosen NK, Herman PMJ, Kromkamp J, Middelburg JJ, Soetaert K (1995) Production and consumption of biological particles in temperate tidal estuaries. https://pure.knaw.nl/portal/en/publications/production-and-consumption-of-biological-particles-in-temperate-tidal-estuaries(766ddea7-098f-4095-b17d-6d4eb2961dcc).html

  • Hondeveld BJM, Nieuwland G, Van Duyl FC, Bak RPM (1995) Impact of nanoflagellate bacterivory on benthic bacterial production in the North Sea. Neth J Sea Res 34:275–287

    Article  Google Scholar 

  • Hubas C, Artigas LF, Davoult D (2007) Role of the bacterial community in the annual benthic metabolism of two contrasted temperate intertidal sites (Roscoff Aber Bay, France). Mar Ecol Prog Ser 344:39–48

    Article  Google Scholar 

  • Hylleberg J (1975) Selective feeding by Abarenicola pacifica with notes on Abarenicola vagabunda and a concept of gardening in lugworms. Ophelia 14:113–137

    Article  Google Scholar 

  • Hylleberg Kristensen J (1972) Carbohydrases of some marine invertebrates with notes on their food and on the natural occurrence of the carbohydrates studied. Mar Biol 14:130–142

    Article  CAS  Google Scholar 

  • Joiris C, Billen G, Lancelot C, Daro MH, Mommaerts JP, Bertels A, Bossicart M, Nijs J, Hecq JH (1982) A budget of carbon cycling in the Belgian coastal zone: relative roles of zooplankton, bacterioplankton and benthos in the utilization of primary production. Neth J Sea Res 16:260–275

    Article  CAS  Google Scholar 

  • Karasov WH, del Rio CM (2007) Physiological ecology: how animals process energy, nutrients, and toxins. Princeton University Press, Princeton

    Google Scholar 

  • Kemp PF (1990) The fate of benthic bacterial production. Aquat Sci 2:109–124

    Google Scholar 

  • Klein Breteler WCM, Schogt N, Baas M, Schouten S, Kraay GW (1999) Trophic upgrading of food quality by protozoans enhancing copepod growth: role of essential lipids. Mar Biol 135:191–198

    Article  Google Scholar 

  • Kristensen E, Penha-Lopes G, Delefosse M, Valdemarsen T, Quintana CO, Banta GT (2012) What is bioturbation? The need for a precise definition for fauna in aquatic sciences. Mar Ecol Prog Ser 446:285–302

    Article  Google Scholar 

  • Kujawinski EB, Longnecker K, Barott KL, Weber RJM, Kido Soule MC (2016) Microbial community structure affects marine dissolved organic matter composition. Front Mar Sci 3:1–15

    Article  Google Scholar 

  • Kuzyakov Y (2010) Priming effects: interactions between living and dead organic matter. Soil Biol Biochem 42:1363–1371

    Article  CAS  Google Scholar 

  • Kuzyakov Y, Friedel JK, Stahr K (2000) Review of mechanisms and quantification of priming effects. Soil Biol Biochem 32:1485–1498

    Article  CAS  Google Scholar 

  • Lacoste É, Piot A, Archambault P, McKindsey CW, Nozais C (2018) Bioturbation activity of three macrofaunal species and the presence of meiofauna affect the abundance and composition of benthic bacterial communities. Mar Environ Res 136:62–70

    Article  CAS  PubMed  Google Scholar 

  • Laverock B, Smith CJ, Tait K, Osborn AM, Widdicombe S, Gilbert JA (2010) Bioturbating shrimp alter the structure and diversity of bacterial communities in coastal marine sediments. ISME J 4:1531–1544

    Article  PubMed  Google Scholar 

  • Laverock B, Gilbert JA, Tait K, Osborn AM, Widdicombe S (2011) Bioturbation: impact on the marine nitrogen cycle. Biochem Soc Trans 39:315–320

    Article  CAS  PubMed  Google Scholar 

  • Laverock B, Kitidis V, Tait K, Gilbert JA, Osborn AM, Widdicombe S (2013) Bioturbation determines the response of benthic ammonia-oxidizing microorganisms to ocean acidification. Philos Trans R Soc B Biol Sci 368:20120441

    Article  CAS  Google Scholar 

  • Lerch TZ, Nunan N, Dignac MF, Chenu C, Mariotti A (2011) Variations in microbial isotopic fractionation during soil organic matter decomposition. Biogeochemistry 106:5–21

    Article  CAS  Google Scholar 

  • Löhnis F (1926) Nitrogen availability of green manures. Soil Sci 22:253–290

    Article  Google Scholar 

  • Lohrer AM, Thrush SF, Hewitt JE, Kraan C (2015) The up-scaling of ecosystem functions in a heterogeneous world. Sci Rep 5. https://doi.org/10.1038/srep10349

  • López-Urrutia Á, Morán XAG (2007) Resource limitation of bacterial production distorts the temperature dependence of oceanic carbon cycling. Ecology 88:817–822

    Article  PubMed  Google Scholar 

  • Luna GM, Manini E, Danovaro R (2002) Large fraction of dead and inactive bacteria in coastal marine sediments: comparison of protocols for determination and ecological significance. Appl Environ Microbiol 68:3509–3513

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Luo Z, Wang E, Smith C (2015) Fresh carbon input differentially impacts soil carbon decomposition across natural and managed systems. Ecology 96:2806–2813

    Article  PubMed  Google Scholar 

  • MacGinitie GE (1932) The role of bacteria as food for bottom animals. Science 76:490

    Article  CAS  PubMed  Google Scholar 

  • Manini E, Fiordelmondo C, Gambi C, Pusceddu A, Danovaro R (2003) Benthic microbial loop functioning in coastal lagoons: a comparative approach. Oceanol Acta 26:27–38

    Article  CAS  Google Scholar 

  • Mann KH (1988) Production and use of detritus in various freshwater, estuarine, and coastal marine ecosystems. Limnol Oceanogr 33:910–930

    CAS  Google Scholar 

  • Mayor DJ, Cook KB, Thornton B, Walsham P, Witte UFM, Zuur AF, Anderson TR (2011) Absorption efficiencies and basal turnover of C, N and fatty acids in a marine Calanoid copepod. Funct Ecol 25:509–518

    Article  Google Scholar 

  • Mayor DJ, Thornton B, Hay S, Zuur AF, Nicol GW, McWilliam JM, Witte UFM (2012a) Resource quality affects carbon cycling in deep-sea sediments. ISME J 6:1740–1748

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mayor DJ, Thornton B, Zuur AF (2012b) Resource quantity affects benthic microbial community structure and growth efficiency in a temperate intertidal mudflat. PLoS One 7:2–7

    Article  CAS  Google Scholar 

  • Mayor DJ, Gray NB, Elver-Evans J, Midwood AJ, Thornton B (2013) Metal-macrofauna interactions determine microbial community structure and function in copper contaminated sediments. PLoS One 8:e64940

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mayor DJ, Sanders R, Giering SLC, Anderson TR (2014) Microbial gardening in the ocean’s twilight zone: detritivorous metazoans benefit from fragmenting, rather than ingesting, sinking detritus. BioEssays 36:1132–1137

    Article  PubMed  PubMed Central  Google Scholar 

  • Mayor DJ, Gray NB, Hattich GSI, Thornton B (2017) Detecting the presence of fish farm-derived organic matter at the seafloor using stable isotope analysis of phospholipid fatty acids. Sci Rep 7:5146

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • McCallister SL, Guillemette F, del Giorgio PA (2006) A system to quantitatively recover bacterioplankton respiratory CO2 for isotopic analysis to trace sources and ages of organic matter consumed in freshwaters. Limnol Oceanogr Methods 4:406–415

    Article  CAS  Google Scholar 

  • Middelburg JJ, Barranguet C, Boschker HTS, Herman PMJ, Moens T, Heip CHR (2000) The fate of intertidal microphytobenthos carbon: an in situ 13C-labeling study. Limnol Oceanogr 45:1224–1234

    Article  CAS  Google Scholar 

  • Miyatake T, Moerdijk-Poortvliet TCW, Stal LJ, Boschker HTS (2014) Tracing carbon flow from microphytobenthos to major bacterial groups in an intertidal marine sediment by using an in situ 13C pulse-chase method. Limnol Oceanogr 59:1275–1287

    Article  CAS  Google Scholar 

  • Moinet GYK, Midwood AJ, Hunt JE, Whitehead D, Hannam KD, Jenkins M, Brewer MJ, Adams MA, Millard P (2018) Estimates of rhizosphere priming effects are affected by soil disturbance. Geoderma 313:1–6

    Article  Google Scholar 

  • Moodley L, Middelburg JJ, Soetaert K, Boschker HTS, Herman PMJ, Heip CHR (2005) Similar rapid response to phytodetritus deposition in shallow and deep-sea sediments. J Mar Res 63:457–469

    Article  CAS  Google Scholar 

  • Moore JC, Berlow EL, Coleman DC, De Suiter PC, Dong Q, Hastings A, Johnson NC, McCann KS, Melville K, Morin PJ, Nadelhoffer K, Rosemond AD, Post DM, Sabo JL, Scow KM, Vanni MJ, Wall DH (2004) Detritus, trophic dynamics and biodiversity. Ecol Lett 7:584–600

    Article  Google Scholar 

  • Moran MA, Kujawinski EB, Stubbins A, Fatland R, Aluwihare LI, Buchan A, Crump BC, Dorrestein PC, Dyhrman ST, Hess NJ, Howe B, Longnecker K, Medeiros PM, Niggemann J, Obernosterer I, Repeta DJ, Waldbauer JR (2016) Deciphering ocean carbon in a changing world. Proc Natl Acad Sci USA 113:3143–3151

    Article  CAS  PubMed  Google Scholar 

  • Mosier A, Kroeze C, Nevison C, Oenema O, Seitzinger S (1998) Closing the global N2O budget : nitrous oxide emissions through the agricultural nitrogen cycle inventory methodology. Nutr Cycling Agroecosyst 52:225–248

    Article  CAS  Google Scholar 

  • Nealson KH (1997) Sediment bacteria: who’s there, what are they doing, and what’s new? Annu Rev Earth Planet Sci 25:403–434

    Article  CAS  PubMed  Google Scholar 

  • Newton J (2016) Stable isotopes as tools in ecological research. eLS. Wiley, Chichester

    Google Scholar 

  • Oakes JM, Eyre BD (2014) Transformation and fate of microphytobenthos carbon in subtropical, intertidal sediments: potential for long-term carbon retention revealed by 13C-labeling. Biogeosciences 11:1927–1940

    Article  CAS  Google Scholar 

  • Oakes JM, Rysgaard S, Glud RN, Eyre BD (2016) The transformation and fate of sub-Arctic microphytobenthos carbon revealed through 13C-labeling. Limnol Oceanogr 61:2296–2308

    Article  CAS  Google Scholar 

  • Pancost RD, Sinninghe Damsté JS (2003) Carbon isotopic compositions of prokaryotic lipids as tracers of carbon cycling in diverse settings. Chem Geol 195:29–58

    Article  CAS  Google Scholar 

  • Parkes RJ, Taylor J (1983) The relationship between fatty acid distributions and bacterial respiratory types in contemporary marine sediments. Estuar Coast Shelf Sci 16

    Article  CAS  Google Scholar 

  • Parkes RJ, Dowling NJE, White DC, Herbert RA, Gibson GR (1993) Characterization of sulphate-reducing bacterial populations within marine and estuarine sediments with different rates of sulphate reduction. FEMS Microbiol Lett 102:235–250

    Article  CAS  Google Scholar 

  • Parr TB, Cronan CS, Ohno T, Findlay SEG, Smith SMC, Simon KS (2015) Urbanization changes the composition and bioavailability of dissolved organic matter in headwater streams. Limnol Oceanogr 60:885–900

    Article  CAS  Google Scholar 

  • Perry GJ, Volkman JK, Johns RB (1979) Fatty acids of bacterial origin in contempary marine sediments. Geochim Cosmochim Acta 43:1715–1725

    Article  CAS  Google Scholar 

  • Peterson BJ, Fry B (1987) Stable isotopes in ecosystem studies. Annu Rev Ecol Syst 18:293–320

    Article  Google Scholar 

  • Phillips NW (1984) Role of different microbes and substrates as potential suppliers of specific, essential nutrients to marine detritivores. Bull Mar Sci 35:283–298

    Google Scholar 

  • Plante CJ, Jumars PA, Baross JA (1990) Digestive associations between marine detritivores and bacteria. Annu Rev Ecol Syst 21:93–127

    Article  Google Scholar 

  • Pomeroy LR, Wiebe WJ (2001) Temperature and substrates as interactive limiting factors for marine heterotrophic bacteria. Aquat Microb Ecol 23:187–204

    Article  Google Scholar 

  • Post DM (2002) Using stable isotopes to estimate trophic position: models, methods, and assumptions. Ecology 83:703–718

    Article  Google Scholar 

  • Pozzato L, Van Oevelen D, Moodley L, Soetaert K, Middelburg JJ (2013) Sink or link? The bacterial role in benthic carbon cycling in the Arabian Sea’s oxygen minimum zone. Biogeosciences 10:6879–6891

    Article  CAS  Google Scholar 

  • Prosser JI, Bohannan BJM, Curtis TP, Ellis RJ, Firestone MK, Freckleton RP, Green JL, Green LE, Killham K, Lennon JJ, Osborn AM, Solan M, van der Gast CJ, Young JPW (2007) The role of ecological theory in microbial ecology. Nat Rev Microbiol 5:384

    Article  CAS  PubMed  Google Scholar 

  • Pusceddu A, Fiordelmondo C, Danovaro R (2005) Sediment resuspension effects on the benthic microbial loop in experimental microcosms. Microb Ecol 50:602–613

    Article  PubMed  Google Scholar 

  • Schmidt JL, Deming JW, Jumars PA, Keil RG (1998) Constancy of bacterial abundance in surficial marine sediments. Limnol Oceanogr 43:976–982

    Article  Google Scholar 

  • Shen H, Jiang G, Wan X, Li H, Qiao Y, Thrush S, He P (2017) Response of the microbial community to bioturbation by benthic macrofauna on intertidal flats. J Exp Mar Biol Ecol 488:44–51

    Article  Google Scholar 

  • Sholkovitz ER (1976) Flocculation of dissolved organic and inorganic matter during the mixing of river water and seawater. Geochim Cosmochim Acta 40:831–845

    Article  CAS  Google Scholar 

  • Smith DJ, Underwood GJC (1998) Exopolymer production by intertidal epipelic diatoms. Limnol Oceanogr 43:1578–1591

    Article  CAS  Google Scholar 

  • Stock W, Heylen K, Sabbe K, Willems A, De Troch M, Savage C (2014) Interactions between benthic copepods, bacteria and diatoms promote nitrogen retention in intertidal marine sediments. PLoS One 9:e111001

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tada K, Koomklang J, Ichimi K, Yamaguchi H (2017) Negligible effect of the benthic fauna on measuring the nutrient upward fluxes from coastal sediments. J Oceanogr 73:397–402

    Article  CAS  Google Scholar 

  • Taylor J, Parkes RJ (1983) The cellular fatty-acids of the sulfate-reducing bacteria, Desulfobacter Sp, Desulfobulbus Sp and Desulfovibrio-Desulfuricans. J Gen Microbiol 129:3303–3309

    CAS  Google Scholar 

  • Teece MA, Fogel ML, Dollhopf ME, Nealson KH (1999) Isotopic fractionation associated with biosynthesis of fatty acids by a marine bacterium under oxic and anoxic conditions. Org Geochem 30:1571–1579

    Article  CAS  Google Scholar 

  • Thornton DCO (2014) Dissolved organic matter (DOM) release by phytoplankton in the contemporary and future ocean. Eur J Phycol 49:20–46

    Article  CAS  Google Scholar 

  • Tunlid A, Ringelberg DB, Phelps TJ, Low C, White DC (1989) Measurement of phospholipid fatty acids at picomolar concentrations in biofilms and deep subsurface sediments using gas chromatography and chemical ionization mass spectrometry. J Microbiol Methods 10:139–153

    Article  CAS  Google Scholar 

  • Underwood GJC, Kromkamp J (1999) Primary production by phytoplankton and microphytobenthos in estuaries. Adv Ecol Res 29:93–153

    Article  CAS  Google Scholar 

  • Van Colen C, Underwood GJC, Serôdio J, Paterson DM (2014) Ecology of intertidal microbial biofilms: mechanisms, patterns and future research needs. J Sea Res 92:2–5

    Article  Google Scholar 

  • Vestal JR, White DC (1989) Lipid analysis in microbial ecology. BioScience 39:535–541

    Article  CAS  PubMed  Google Scholar 

  • White DC (1988) Validation of quantitative analysis for microbial biomass, community structure, and metabolic activity. Arch Hydrobiol 31:1–18

    Google Scholar 

  • White DC, Davis WM, Nickels JS, King JD, Bobbie RJ (1979) Determination of the sedimentary microbial biomass by extractible lipid phosphate. Oecologia 40:51–62

    Article  CAS  PubMed  Google Scholar 

  • White DC, Stair JO, Ringelberg DB (1996) Quantitative comparisons of in situ microbial biodiversity by signature biomarker analysis. J Ind Microbiol 17:185–196

    Article  CAS  Google Scholar 

  • Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95:6578–6583

    Article  CAS  PubMed  Google Scholar 

  • Yingst JY, Rhoads DC (1980) The role of bioturbation in the enhancement of bacterial growth rates in marine sediments. Marine benthic dynamics. University of South Carolina Press, Columbia

    Google Scholar 

  • Zetsche E, Thornton B, Midwood AJ, Witte U (2011) Utilisation of different carbon sources in a shallow estuary identified through stable isotope techniques. Cont Shelf Res 31:832–840

    Article  Google Scholar 

  • ZoBell CE, Feltham CB (1942) The bacterial flora of a marine mud flat as an ecological factor. Ecology 23:69–78

    Article  Google Scholar 

  • Zou K, Thébault E, Lacroix G, Barot S (2016) Interactions between the green and brown food web determine ecosystem functioning. Funct Ecol 30:1454–1465

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. National Oceanography Centre, Southampton, UK

    Daniel J. Mayor

  2. James Hutton Institute, Aberdeen, UK

    Daniel J. Mayor & Barry Thornton

  3. University of Southampton, Southampton, UK

    Daniel J. Mayor, Holly Jenkins & Stacey L. Felgate

Authors
  1. Daniel J. Mayor
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Barry Thornton
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Holly Jenkins
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Stacey L. Felgate
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Daniel J. Mayor .

Editor information

Editors and Affiliations

  1. MMS, Faculté des Sciences, Université de Nantes, Nantes, France

    Peter G. Beninger

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Mayor, D.J., Thornton, B., Jenkins, H., Felgate, S.L. (2018). Microbiota: The Living Foundation. In: Beninger, P. (eds) Mudflat Ecology. Aquatic Ecology Series, vol 7. Springer, Cham. https://doi.org/10.1007/978-3-319-99194-8_3

Download citation

Publish with us

Policies and ethics

Search

Navigation