The calc_nemindex() is used to Calculate multiple nematode ecological
indices and generate nemindex-class. The ecological indexes that
can be calculated by this function include MI, sigMI, sigMI25,
MI25, PPI, WI, NCR, CI, BI, SI,
EI, etc.
calc_nemindex(data)A nemindex-class for storing nematode ecological indices
analysis results.
MI, Maturity Index. Indicates environmental disturbance resulting from
perturbations (range, 1-5). Low values (<2) indicate an early (primary or secondary)
successional stage or a temporary level of increased nutrient availability.
Values close to 2 indicate a high level of disturbance with low soil food web
structure, while intermediate values (2.5–3) indicate some soil food web maturity.
High values (>3) indicate a well-structured and complex soil food web likely with
connectivity and energy flow between trophic levels.
sigMI, Sigma Maturity Index (SigmaMI). Indicates environmental disturbance
resulting from perturbations in non-agricultural soils (range, 1-5). Low values (<2)
indicate a high level of nutrient availability and minimal plant-parasitic pressure,
while values close to 2 indicate a high level of disturbance with low soil food web
structure. Intermediate values (2.5–3) indicate some soil food web maturity.
High values (>3), in turn, indicate a well-structured and complex soil food web
likely with connectivity and energy flow between trophic levels, which might include
larger plant-parasitic nematodes. This index is less sensitive to enrichment in
agricultural soils.
sigMI25, Sigma Maturity Index 2-5 (SigmaMI25). computes the MI for all
nematodes in the c-p2-5 range (Neher & Campbell, 1996). The index recognizes
that the higher c-p value plant-feeding species also provide information of
environmental stress but bears some of the burden of the SigmaMI in situations of
nutrient enrichment.
MI25, Maturity Index 2–5. Indicates Environmental disturbance resulting
from perturbations unrelated to nutrient enrichment in agricultural fields (range, 2-5).
Low values (close to 2) indicate substantial disturbance resulting from perturbations
unrelated to nutrient enrichment. High values (>3) indicate greater maturity with
minimal or no effect resulting from perturbations.
PPI, Plant-Parasitic Index. Indicates Assemblage composition of plant-parasitic
nematodes (range, 2-5). Low values (close to 2) indicate plant-parasitic nematode
assemblages dominated by small and medium-sized ectoparasites that feed on single
plant cells. Higher values indicate assemblages dominated by medium and large (semi-)
endoparasitic (e.g., Meloidogyne and Heterodera spp.) or ectoparasitic virus transmitting
nematodes (e.g., Xiphinema and Longidorus spp.).
PPI_MI, PPI/MI. The PPI/MI ratio is lower under nutrient poor conditions
than under nutrient rich conditions. It is a sensitive indicator of enrichment
in agroecosystems (Bongers & Korthals, 1995; Bongers et al., 1997).
WI, Wasilewska Index. Wasilewska Index is calculated by dividing the
sum of bacteria-feeding nematodes and fungi-feeding nematodes by the number of
herbivorous nematodes. This index is used to indicate the impact of nematode communities
on crop production. The smaller the index, the greater the negative impact of nematode
communities on crop production.
NCR, Nematode Channel Ratio. The Nematode Channel Ratio (NCR) is a parameter
used in soil ecology to assess the balance between bacterial and fungal energy
channels in the soil food web. This ratio is calculated by comparing the abundance
of bacterial-feeding nematodes to fungal-feeding nematodes. High NCR: Indicates
a bacterial-dominated energy channel. This is often found in soils with frequent
disturbance or high inputs of easily decomposable organic matter. Low NCR: Indicates
a fungal-dominated energy channel. This is commonly found in more stable, less
disturbed soils, such as forests or natural grasslands, where organic matter
decomposition is slower and more complex.
CI, Channel Index. Indicates predominant decomposition pathway of organic matter (range, 0-100).
Lower values (<50) indicate increasing decomposition dominance by bacteria, while
higher values (>50) indicate increasing decomposition dominance by fungi. Bacterial
dominance indicates the presence of rapidly decomposed organic matter, while fungal
dominated decomposition indicates the slow breakdown of more complex organic matter.
The focus on opportunistic bacterial and fungal feeders makes this a highly responsive
index, which can be used to detect alternating decomposition pathways over time.
EI, Enrichment Index. Indicates food availability and nutrient enrichment
(range, 0-100). Low (0–30), intermediate (30–60), and high (60–100) values indicate
equivalent levels of food availability (e.g., labile organic carbon) and nutrient enrichment.
SI, Structure Index. Indicates Soil food web structure and complexity,
as well as disturbance due to environmental (e.g., salinity and drought) or
anthropogenic (e.g. tillage, mining, and chemical pollution) causalities (range, 0-100).
Low (0–30), intermediate (30–60), and high (60–100) values indicate equivalent levels
of soil food web complexity. Lower values are indicative of perturbed soil food webs,
while higher values indicate a structured soil food web.
BI, Basal Index. Indicates food web structure and complexity (range, 0-100).
Low (0–30), intermediate (30–60), and high (60–100) values indicate equivalent
levels of soil perturbation. Therefore, higher values (>50) are indicative of
a depleted and damaged soil food web.
TotalBiomass, Total biomass of nematode community.
MetabolicFootprint, Metabolic Footprints. Indicates magnitude of
ecosystem functions and services fulfilled by nematode community (range, 0-infinite).
Higher metabolic footprint values are indicative of greater carbon channelling
and therefore an increased contribution to the fulfilment of soil ecosystem
functions and services. This can be considered per trophic group (e.g. bacterivore
footprint), or per component of the nematode community that indicate enrichment
(enrichment footprint) and structure (structure footprint).
EnrichmentFootprint, Enrichment Footprint.
StructureFootprint, Structure Footprint.
HerbivoreFootprint, Herbivore Footprint.
FungivoreFootprint, Fungivore Footprint
BacterivoreFootprint, Bacterivore Footprint.
PrOmFootprint, Metabolic footprint of an omnivorous predatory nematode.
Numbers, Number of nematodes.
CAssimilated, Carbon assimilated by nematodes.
CRespired, Carbon consumed by nematode respiration.
An easynem-class data.
To facilitate code interpretation, it is recommended to use the pipe symbol
|> to connect functions:
nem_index <- nem |> calc_nemindex()
http://nemaplex.ucdavis.edu/Ecology/Indices_of_ecosystem_condition.html
Du Preez G, Daneel M, De Goede R, et al. Nematode-based indices in soil ecology: Application, utility, and future directions. Soil Biology and Biochemistry, 2022, 169: 108640.
Bongers T. The maturity index: an ecological measure of environmental disturbance based on nematode species composition. Oecologia, 1990, 83: 14-19.
Bongers T, Goede R G N, Korthals G W, et al. Proposed changes of cp classification for nematodes. 1995.
Ferris, H. O. W. A. R. D., and Tom Bongers. "Indices developed specifically for analysis of nematode assemblages." Nematodes as environmental indicators. Wallingford UK: CABI, 2009. 124-145.
Goede, RGM de, T. Bongers, and C. H. Ettema. "Graphical presentation and interpretation of nematode community structure: cp triangles." (1993): 743-750.
Ferris, Howard, Tom Bongers, and Ron GM de Goede. "A framework for soil food web diagnostics: extension of the nematode faunal analysis concept." Applied soil ecology 18.1 (2001): 13-29.
Ferris, Howard. "Form and function: metabolic footprints of nematodes in the soil food web." European Journal of Soil Biology 46.2 (2010): 97-104.
Other functions in this R package for data calculations:
calc_beta2, calc_compare, calc_compare2,
calc_beta, calc_alpha, calc_funguild,
calc_funguild2, calc_mf, calc_mf2,
calc_ter, calc_ter2, calc_ef,
calc_ef2.
nem <- read_nem2(tab = nemtab, tax = nemtax, meta = nemmeta)
nem_index <- nem |> calc_nemindex()
show(nem_index)
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