Relationships between labile soil organic matter and nematode communities in a California oak woodland

in Nematology
Restricted Access
Get Access to Full Text
Rent on DeepDyve

Have an Access Token?

Enter your access token to activate and access content online.

Please login and go to your personal user account to enter your access token.


Have Institutional Access?

Access content through your institution. Any other coaching guidance?


Labile soil organic matter (SOM) is an important energy source for below-ground ecosystems but the association of labile SOM and nematode communities is poorly characterised. In this study, soil nematode communities and nematode-derived indices of ecosystem function were characterised and related to SOM lability in an undisturbed riparian woodland (California, USA). SOM lability was assessed by microbial biomass C (MBC), permanganate-oxidisable C (POXC), extractable organic C (EOC), and diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy. The channel index, which measures the ratio of bacterial-feeding to fungal-feeding nematodes in cp groups 1 and 2, respectively, decreased with labile C fractions and aliphatic C-H enrichment (infrared absorbance at 2920 cm−1) but increased with aromatic C=C enrichment (1620 cm−1) and index of decomposition (2930:1620 cm−1), as did the nematode structure index. These results indicate that nematode communities respond to variation in labile C fractions and SOM composition across a heterogeneous natural landscape, which may reflect observed differences in SOM lability among woody plant species.

Relationships between labile soil organic matter and nematode communities in a California oak woodland

in Nematology



AmiD.NatalelloA.ZulliniA.DogliaS.M. (2004). Fourier transform infrared microspectroscopy as a new tool for nematode studies. FEBS Letters 576297-300.

BarkerK.R. (1985). Nematode extraction and bioassays. In: BarkerK.R.CarterC.R.SasserJ.N. (Eds). An advanced treatise on Meloidogyne. Raleigh, NC, USANorth Carolina State University Graphics.

BarthèsB.G.BrunetD.RabaryB.BaO.VillenaveC. (2011). Near infrared reflectance spectroscopy (NIRS) could be used for characterization of soil nematode community. Soil Biology and Biochemistry 431649-1659.

BlairG.LefroyR.LisleL. (1995). Soil carbon fractions based on their degree of oxidation, and the development of a carbon management index for agricultural systems. Australian Journal of Agricultural Research 461459-1466.

BongersT. (1990). The maturity index: an ecological measure of environmental disturbance based on nematode species composition. Oecologia 8314-19.

BongersT.FerrisH. (1999). Nematode community structure as a bioindicator in environmental monitoring. Trends in Ecology & Evolution 14224-228. GoedeR.G.M.KorthalsG.YeatesG.W. (1995). Proposed changes of c-p classification for nematodes. Russian Journal of Nematology 361-62.

BouwmanL.A.ZwartK.B. (1994). Soil ecology of conventional and integrated arable farming systems; the ecology of bacterivorous protozoans and nematodes in arable soil. Agriculture Ecosystems & Environment 51145-160.

BriarS.S.JagdaleG.B.ChengZ.HoyC.W.MillerS.A.GrewalP.S. (2007). Indicative value of soil nematode food web indices and trophic group abundance in differentiating habitats with a gradient of anthropogenic impact. Environmental Bioindicators 2146-160.

CalderónF.J.MikhaM.M.VigilM.F.NielsenD.C.BenjaminJ.G.ReevesJ.B. (2011a). Diffuse-reflectance mid-infrared spectral properties of soils under alternative crop rotations in a semi-arid climate. Communications in Soil Science and Plant Analysis 422143-2159.

CalderónF.J.ReevesJ.B.CollinsH.P.PaulE.A. (2011b). Chemical differences in soil organic matter fractions determined by diffuse-reflectance mid-infrared spectroscopy. Soil Science Society of America Journal 75568-579.

ChauvinC.DorelM.VillenaveC.Roger-EstradeJ.ThuriesL.RisèdeJ.-M. (2015). Biochemical characteristics of cover crop litter affect the soil food web, organic matter decomposition, and regulation of plant-parasitic nematodes in a banana field soil. Applied Soil Ecology 96131-140.

CulmanS.W.DupontS.T.GloverJ.D.BuckleyD.H.FickG.W.FerrisH.CrewsT. (2010). Long-term impacts of high-input annual cropping and unfertilized perennial grass production on soil properties and belowground food webs in Kansas, USA. Agriculture Ecosystems & Environment 13713-24.

CulmanS.W.SnappS.S.FreemanM.A.SchipanskiM.E.BenistonJ.LalR.DrinkwaterL.E.FranzluebbersA.J.GloverJ.D.GrandyA.S. (2012). Permanganate oxidizable carbon reflects a processed soil fraction that is sensitive to management. Soil Science Society of America Journal 76494-504.

CulmanS.W.SnappS.S.GreenJ.M.GentryL.E. (2013). Short- and long-term labile soil carbon and nitrogen dynamics reflect management and predict corn agronomic performance. Agronomy Journal 105493-502.

DahlgrenR.A.HorwathW.R.TateK.W.CampingT.J. (2003). Blue oak enhance soil quality in California oak woodlands. California Agriculture 5742-47.

DalalR.C. (1998). Soil microbial biomass; what do the numbers really mean? Australian Journal of Experimental Agriculture 38649-665.

DemyanM.S.RascheF.SchulzE.BreulmannM.MüllerT.CadischG. (2012). Use of specific peaks obtained by diffuse reflectance Fourier transform mid-infrared spectroscopy to study the composition of organic matter in a Haplic Chernozem. European Journal of Soil Science 63189-199.

DillyO.IrmlerU. (1998). Succession in the food web during the decomposition of leaf litter in a black alder (Alnus glutinosa (Gaertn.) L.) forest. Pedobiologia 42109-123.

DupontS.T.CulmanS.W.FerrisH.BuckleyD.H.GloverJ.D. (2010). No-tillage conversion of harvested perennial grassland to annual cropland reduces root biomass, decreases active carbon stocks, and impacts soil biota. Agriculture Ecosystems & Environment 13725-32.

ErhagenB.ÖquistM.SparrmanT.HaeiM.IlstedtU.HedenströmM.SchleucherJ.NilssonM.B. (2013). Temperature response of litter and soil organic matter decomposition is determined by chemical composition of organic material. Global Change Biology 193858-3871.

ErnakovichJ.G.WallensteinM.D.CalderónF.J. (2015). Chemical indicators of cryoturbation and microbial processing throughout an Alaskan permafrost soil depth profile. Soil Science Society of America Journal 79784-793 DOI:10.2136/sssaj2014.10.0420.

EshelG.LevyG.J.MingelgrinU.SingerM.J. (2004). Critical evaluation of the use of laser diffraction for particle-size distribution analysis. Soil Science Society of America Journal 68736-743.

EssingtonM.E. (2004). Soil and water chemistry: an integrative approach. Boca Raton, FL, USACRC Press.

FerrisH. (2010). Contribution of nematodes to the structure and function of the soil food web. Journal of Nematology 4263-67.

FerrisH.MatuteM.M. (2003). Structural and functional succession in the nematode fauna of a soil food web. Applied Soil Ecology 2393-110.

FerrisH.BongersT. (2006). Nematode indicators of organic enrichment. Journal of Nematology 383-12.

FerrisH.VenetteR.C.LauS.S. (1996). Dynamics of nematode communities in tomatoes grown in conventional and organic farming systems, and their impact on soil fertility. Applied Soil Ecology 3161-175.

FerrisH.BongersT.De GoedeR.G.M. (2001). A framework for soil food web diagnostics: extension of the nematode faunal analysis concept. Applied Soil Ecology 1813-29.

FosterJ.C. (1995). Soil nitrogen. In: AlefK.NannipieriP. (Eds). Methods in applied soil microbiology and biochemistry. San Diego, CA, USAAcademic Press.

FranklandJ.C. (1998). Fungal succession – unravelling the unpredictable. Mycological Research 1021-15.

GiacomettiC.DemyanM.S.CavaniL.MarzadoriC.CiavattaC.KandelerE. (2013). Chemical and microbiological soil quality indicators and their potential to differentiate fertilization regimes in temperate agroecosystems. Applied Soil Ecology 6432-48.

GrandyA.S.NeffJ.C. (2008). Molecular C dynamics downstream: the biochemical decomposition sequence and its impact on soil organic matter structure and function. Science of the Total Environment 404297-307.

GrossoF.BååthE.De NicolaF. (2016). Bacterial and fungal growth on different plant litter in Mediterranean soils: effects of C/N ratio and soil pH. Applied Soil Ecology 1081-7.

HodsonA.K.FerrisH.HollanderA.D.JacksonL.E. (2014). Nematode food webs associated with native perennial plant species and soil nutrient pools in California riparian oak woodlands. Geoderma 228-229182-191.

HsuJ.-H.LoS.-L. (1999). Chemical and spectroscopic analysis of organic matter transformations during composting of pig manure. Environmental Pollution 104189-196.

InbarY.ChenY.HadarY. (1989). Solid-state carbon-13 nuclear magnetic resonance and infrared spectroscopy of composted organic matter. Soil Science Society of America Journal 531695-1701.

LeonowiczA.ChoN.LuterekJ.WilkolazkaA.Wojtas-WasilewskaM.MatuszewskaA.HofrichterM.WesenbergD.RogalskiJ. (2001). Fungal laccase: properties and activity on lignin. Journal of Basic Microbiology 41185-227.

LiangC.BalserT.C. (2011). Microbial production of recalcitrant organic matter in global soils: implications for productivity and climate policy. Nature Reviews Microbiology 975.

MäkeläM.R.MarinovićM.NousiainenP.LiwanagA.J.M.BenoitI.SipiläJ.HatakkaA.De VriesR.P.HildénK.S. (2015). Aromatic metabolism of filamentous fungi in relation to the presence of aromatic compounds in plant biomass. In: SimaS.Geoffrey MichaelG. (Eds). Advances in applied microbiology. New York, NY, USAAcademic Press pp.  63-137.

MargenotA.J.CalderónF.J.BowlesT.M.ParikhS.J.JacksonL.E. (2015). Soil organic matter functional group composition in relation to organic carbon, nitrogen, and phosphorus fractions in organically managed tomato fields. Soil Science Society of America Journal 79772-782.

MarschnerB.KalbitzK. (2003). Controls of bioavailability and biodegradability of dissolved organic matter in soils. Geoderma 113211-235.

MeierC.L.BowmanW.D. (2008). Links between plant litter chemistry, species diversity, and below-ground ecosystem function. Proceedings of the National Academy of Sciences of the United States of America 10519780-19785.

MirandaK.M.EspeyM.G.WinkD.A. (2001). A rapid, simple spectrophotometric method for simultaneous detection of nitrate and nitrite. Nitric Oxide 562-71.

NilesR.K.FreckmanD.W. (1998). From the ground up: nematode ecology in bioassessment and ecosystem health. In: BarkerK.PedersonG.WindhamG. (Eds). Plant and nematode interactions. Madison, WI, USAAmerican Sociery of Agronomy pp.  65-85.

NorthupR.R.YuZ.DahlgrenR.A.VogtK.A. (1995). Polyphenol control of nitrogen release from pine litter. Nature 377227-229.

OkadaH.KadotaI. (2003). Host status of 10 fungal isolates for two nematode species, Filenchus misellus and Aphelenchus avenae. Soil Biology and Biochemistry 351601-1607.

OkadaH.TsukiboshiT.KadotaI. (2002). Mycetophagy in Filenchus misellus (Andrássy, 1958) Raski & Geraert, 1987 (Nematoda: Tylenchidae), with notes on its morphology. Nematology 4795-801.

OkadaH.HaradaH.KadotaI. (2005). Fungal-feeding habits of six nematode isolates in the genus Filenchus. Soil Biology and Biochemistry 371113-1120.

PanettieriM.KnickerH.MurilloJ.M.MadejónE.HatcherP.G. (2014). Soil organic matter degradation in an agricultural chronosequence under different tillage regimes evaluated by organic matter pools, enzymatic activities and CPMAS 13C NMR. Soil Biology and Biochemistry 78170-181.

PanettieriM.BernsA.E.KnickerH.MurilloJ.M.MadejónE. (2015). Evaluation of seasonal variability of soil biogeochemical properties in aggregate-size fractioned soil under different tillages. Soil and Tillage Research 15139-49.

ParikhS.J.GoyneK.W.MargenotA.J.MukomeF.N.D.CalderónF.J. (2014). Soil chemical insights provided through vibrational spectroscopy. In: DonaldL.S. (Ed.). Advances in agronomy. New York, NY, USAAcademic Press pp.  1-148.

Plaza-BonillaD.Álvaro-FuentesJ.Cantero-MartínezC. (2014). Identifying soil organic carbon fractions sensitive to agricultural management practices. Soil and Tillage Research 13919-22.

R Development Core Team (2014). R: a language and enviroment for statistical computing. Vienna, AustriaR Foundation for Statistical Computing. Available online at

RineauF.RothD.ShahF.SmitsM.JohanssonT.CanbäckB.OlsenP.B.PerssonP.GrellM.N.LindquistE. (2012). The ectomycorrhizal fungus Paxillus involutus converts organic matter in plant litter using a trimmed brown-rot mechanism involving Fenton chemistry. Environmental Microbiology 141477-1487.

RosG.H.HofflandE.Van KesselC.TemminghoffE.J.M. (2009). Extractable and dissolved soil organic nitrogen – a quantitative assessment. Soil Biology and Biochemistry 411029-1039.

RosenbrockP.BuscotF.MunchJ. (1995). Fungal succession and changes in the fungal degradation potential during the initial stage of litter decomposition in a black alder forest (Alnus glutinosa (L.) Gaertn.). European Journal of Soil Biology 311-11.

RossettiI.BagellaS.CappaiC.CariaM.C.LaiR.RoggeroP.P.Martins Da SilvaP.SousaJ.P.QuernerP.SeddaiuG. (2015). Isolated cork oak trees affect soil properties and biodiversity in a Mediterranean wooded grassland. Agriculture Ecosystems & Environment 202203-216.

RuessL.FerrisH. (2004). Decomposition pathways and successional changes. In: CookR.HuntD.J.CookR.HuntD.J.). Leiden, The NetherlandsBrill pp.  547-556.

San-BlasE.GuerraM.PortilloE.EstevesI.CubillánN.AlvaradoY. (2011). ATR/FTIR characterization of Steinernema glaseri and Heterorhabditis indica. Vibrational Spectroscopy 57220-228.

Sánchez-MorenoS.NicolaN.L.FerrisH.ZalomF.G. (2009). Effects of agricultural management on nematode-mite assemblages: soil food web indices as predictors of mite community composition. Applied Soil Ecology 41107-117.

Sánchez-MorenoS.FerrisH.Young-MathewsA.CulmanS.W.JacksonL.E. (2011). Abundance, diversity and connectance of soil food web channels along environmental gradients in an agricultural landscape. Soil Biology and Biochemistry 432374-2383.

ScheuS.RuessL.BonkowskiM. (2005). Interactions between micro-organisms and soil micro- and mesofauna. In: BuscotF.VarmaS. (Eds). Micro-organisms in soils: roles in genesis and functions. Heidelberg, GermanySpringer pp.  253-275.

SchmidtM.W.I.TornM.S.AbivenS.DittmarT.GuggenbergerG.JanssensI.A.KleberM.Kogel-KnabnerI.LehmannJ.ManningD.A.C. (2011). Persistence of soil organic matter as an ecosystem property. Nature 47849-56.

ShengM.GorzsásA.TuckS. (2016). Fourier transform infrared microspectroscopy for the analysis of the biochemical composition of C. elegans worms. Worm 5e1132978.

SixJ.FreyS.D.ThietR.K.BattenK.M. (2006). Bacterial and fungal contributions to carbon sequestration in agroecosystems. Soil Science Society of America Journal 70555-569 DOI:10.2136/sssaj2004.0347.

SmidtE.LechnerP.SchwanningerM.HaberhauerG.GerzabekM.H. (2002). Characterization of waste organic matter by FT-IR spectroscopy: application in waste science. Applied Spectroscopy 561170-1175.

SparlingG. (1992). Ratio of microbial biomass carbon to soil organic carbon as a sensitive indicator of changes in soil organic matter. Soil Research 30195-207. la PeñaE.FonderieP.WillekensK.BorgonieG.BertW. (2010). Nematode succession during composting and the potential of the nematode community as an indicator of compost maturity. Pedobiologia 53181-190.

UgarteC.M.ZaborskiE.R.WanderM.M. (2013). Nematode indicators as integrative measures of soil condition in organic cropping systems. Soil Biology and Biochemistry 64103-113.

VanceE.D.BrookesP.C.JenkinsonD.S. (1987). An extraction method for measuring soil microbial biomass C. Soil Biology and Biochemistry 19703-707.

VerchotL.V.DutaurL.ShepherdK.D.AlbrechtA. (2011). Organic matter stabilization in soil aggregates: understanding the biogeochemical mechanisms that determine the fate of carbon inputs in soils. Geoderma 161182-193.

VeumK.GoyneK.KremerR.MilesR.SudduthK. (2014). Biological indicators of soil quality and soil organic matter characteristics in an agricultural management continuum. Biogeochemistry 11781-99.

WardleD.A.BardgettR.D.KlironomosJ.N.SetäläH.van der PuttenW.H.WallD.H. (2004). Ecological linkages between aboveground and belowground biota. Science 3041629-1633.

WeilR.R.IslamK.R.StineM.A.GruverJ.B.Samson-LiebigS.E. (2003). Estimating active carbon for soil quality assessment: a simplified method for laboratory and field use. American Journal of Alternative Agriculture 183-17.

WrightC.J.ColemanD.C. (2000). Cross-site comparison of soil microbial biomass, soil nutrient status, and nematode trophic groups. Pedobiologia 442-23. GoedeR.G.M.FreckmanD.W.GeorgievaS.S. (1993). Feeding habits in soil nematode families and genera – an outline for soil ecologists. Journal of Nematology 25315-331.


  • View in gallery

    Nematode food web analysis of taxa isolated from surface soils (0-7.5 cm) in riparian woodland at the Audubon Bobcat Ranch Reserve in Yolo County, CA, USA. Communities with enrichment indices (EI) over 50 are considered more N-enriched, whilst those with structure indices over 50% are either mature or maturing. Symbols represent different tree species, circle = blue oak, triangle = live oak, square = manzanita, x = redbud, and circle within a square = toyon.

  • View in gallery

    Principle components analysis of nematode indices, carbon pools and average band areas corresponding to specific soil organic matter (SOM) functional groups. CI = Nematode Channel Index, SI = Nematode Structure Index, EI = Nematode Enrichment Index. The band area centred at 1620 cm−1 ranges from 1660-1580 cm−1 and corresponds to aromatic C=C,with potential contributions from amide C=O. The band centred at 2920 cm−1 ranges from 3010-2810 cm−1 and corresponds to aliphatic C-H. The humification index, or HI, is the ratio of two band areas (1620 cm−1:2930 cm−1) and increases with the degree of decomposition.

  • View in gallery

    Correlation coefficient (Pearson R) between nematode indices and absorbance of surface soils (n = 50) measured by diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy. SI = nematode Structure Index, which increases with the proportion of predators and indicates more mature communities. CI = nematode Channel Index, which measures the ratio of fungal feeders to bacterial-feeders in the population in cp groups 1 and 2, respectively. Soil samples (0-7.5 cm depth) are from undisturbed riparian woodland at the Audubon Bobcat Ranch Reserve in Yolo County, CA, USA. This figure is published in colour in the online edition of this journal, which can be accessed via

Index Card

Content Metrics

Content Metrics

All Time Past Year Past 30 Days
Abstract Views 21 21 15
Full Text Views 2 2 2
PDF Downloads 0 0 0
EPUB Downloads 0 0 0