Biotic indices based on soil nematode communities for assessing soil quality in terrestrial ecosystems

Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap

A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or "in development", hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.

Seasonal Stabilities of Soil Nematode Communities and Their Relationships with Environmental Factors in Different Temperate Forest Types on the Chinese Loess Plateau

The bottom-up effects of vegetation have been documented to be strong drivers of the soil food web structure and functioning in temperate forests. However, how the forest type affects the stability of the soil food web is not well known. In the Ziwuling forest region of the Loess Plateau, we selected three typical forests, Pinus tabuliformis Carrière (PT), Betula platyphylla Sukaczev (BP), and Quercus liaotungensis Koidz. (QL), to investigate the soil nematode community characteristics in the dry (April) and rainy (August) season, and analyzed their relationships with the soil properties. The results showed that the characteristics of the soil nematode communities and their seasonal variations differed markedly among the forest types. Compared to P. tabuliformis (PT), the B. platyphylla (BP) and Q. liaotungensis (QL) forests had higher plant diversity and more easily decomposed litters, which were more effective for improving the soil resource availability, thus, leading to more beneficial effects on the soil nematode community. In both the dry and rainy season, the soil nematode abundance was the highest in the BP forest. The Shannon–Wiener diversity index (H’), Pielou’s evenness index (J’), and nematode channel ratio index (NCR) were higher, while the Simpson dominance index (λ) and plant parasite index (PPI) were lower, in the BP and QL forests compared with in the PT forest. From the dry to rainy season, the total nematode abundance and the abundance of fungivores, bacterivores, and omnivore-predators, significantly increased in the QL and PT forests, and the values of the Wasilewska index (WI), maturity index (MI), H’, J’, λ, and NCR showed the most significant seasonal variability in the PT forest, which were mainly driven by changes in the soil labile C and N and the moisture content between the two seasons. Generally, the seasonal stability of the soil nematode communities was the highest in the BP forest and the poorest in the PT forest, probably due to variations in the plant diversity. Our results suggest the importance of tree species and diversity as bottom-up regulating factors of the soil food web structure, function, and seasonal stability, which has important implications for sustainable forest management in the Loess Plateau and other temperate regions.

Short-Time Impact of Soil Amendments with Medicago Plant Materials on Soil Nematofauna

Soil amendments with plant materials from Medicago species are widely acknowledged for a suppressive effect on plant-parasitic nematodes but their impact on beneficial components of soil nematofauna is still unknown. A study on potted tomato was carried out to investigate the short-time effects on the overall nematofauna of dry biomasses from six different Medicago species, i.e., M. sativa, M. heyniana, M. hybrida, M. lupulina, M. murex and M. truncatula, incorporated to natural soil at 10, 20, or 40 g kg⁻¹ soil rates. All amendments resulted in a significant decrease of the total nematofauna biomass, whereas total abundance was significantly reduced only by M. heyniana, M. hybrida, and M. lupulina biomasses. Almost all the Medicago amendments significantly reduced the relative abundance of plant-parasites and root fungal feeders. All amendments significantly increased the abundance of bacterivores, whereas fungivores significantly increased only in soil amended with M. heyniana, M. lupulina and M. sativa plant materials. Mesorhabditis and Rhabditis were the most abundant genera of bacterivores, whereas Aphelenchoides and Aphelenchus prevailed among the fungivores. Predators were poorly influenced by all the tested Medicago biomasses, whereas the abundance of omnivores was negatively affected by M. heyniana and M. lupulina. Values of the Maturity Index and Sum Maturity Index were reduced by treatments with M. heyniana, M. hybrida, M. lupulina and M. sativa plant materials, whereas most of the tested amendments decreased values of the Channel Index while increasing those of the Enrichment Index. Enrichment and bacterivore footprints raised following soil addition with Medicago biomasses, whereas composite and fungivore footprints were significantly reduced. According to their overall positive effects on soil nematofauna, amendments with Medicago plant materials or their formulated derivatives could represent an additional tool for a sustainable management of plant-parasitic nematodes.

Nematode communities as indicators of the status of a soil ecosystem influenced by mining practices in Brazil

This study evaluated the effects of mining practices using soil nematodes as bioindicators. Soil samples represented four different subsystems found in the CeBio Research Center, including natural/undisturbed (rainforest (RF) and savannah (SA)) and disturbed (Eucalyptus spp. (EU) and grassland (GR)) subsystems. Ecological descriptors S (3.5-9.5), d (1.22-4.23) and MI (1.9-3.23) significantly differentiated the subsystem GR (high impact) from the other subsystems. Additionally, poorly covered soil (i.e., subsystem GR) negatively influenced the composition of nematode assemblages, and primarily so for nematodes with high c-p values. Among soil variables, pH strongly influenced the distribution of soil nematodes, negatively affecting the abundance of all c-p groups and diversity of nematodes. On the other hand, pH also positively affected FF and PP trophic groups in the subsystem GR. The similarity of subsystem EU and natural subsystems (RF and SA) suggests that soil restoration with Eucalyptus spp. appears to be an adequate management practice to promote the recovery of areas subjected to mining practices.

Nematodes as bioindicators of ecosystem recovery during phytoremediation of crude oil contaminated soil

Restoration of a weathered crude oil contaminated site undergoing phytoremediation was evaluated using nematodes as bioindicators. Samples were collected twice per year equating to spring and fall/winter. Mean annual total abundances ranged from 18-130 in the non-fertilized non-vegetated control (CTR) to 69-728 in tall fescue-ryegrass (FES) to 147-749 (100 g(-1)) in the fertilized bermudagrass-fescue (BER) treatment. Proportions of plant-parasitic (PP) and free-living (FL) nematodes were significantly impacted by treatment, but not year, with PP nematodes accounting for 27, 59, and 68% of CTR, FES, and BER communities, respectively. There was no significant year by season by treatment or treatment by year effect for total, PP, or FL nematode abundances. Diversity did not increase over time. The BER and FES treatments had more mature communities as indicated by higher plant-parasitic index (PPI) values. Phytoremediation accelerates petroleum degradation and alters the soil habitat which is reflected in the nematode community. However, low numbers and inconsistent presence of persister strategist omnivores and predators, and the lack in improvement over time in treatment effects for total and PP nematode abundances, PP and FL proportions, or PPI indicate the system is being rehabilitated but has not been restored after 69 months of phytoremediation.

Phytoremediation of soils co-contaminated by organic compounds and heavy metals: bioassays with Lupinus luteus L. and associated endophytic bacteria

In the central part of the Iberian Peninsula there are old sealed landfills containing soils co-contaminated by several heavy metals (Cu, Zn, Pb, Cd, Ni, As, Cr, Fe, Al, Mn) and organic pollutants of different families (hydrocarbons, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, pesticides and other organochlorinated compounds, phenols and volatile compounds), which this work will address. We have focused on phytoremedial plants that are able to deal with this type of complex pollution, not only species that tolerate the joint effect of heavy metals in the soil, but also those that can take advantage of associated bacteria to efficiently break down organic compounds. This study was carried out with Lupinus luteus and its endophytes in two greenhouse experiments: A) growing in a substrate artificially contaminated with benzo(a)pyrene (BaP), and B) using real co-contaminated landfill soils. Endophytes of roots and shoots were isolated in both bioassays. Plant growth-promotion tests and organic pollutant tolerance and degradation tests were conducted on all strains isolated in bioassay A), and on those proving to be pure cultures from bioassay B). The selected landfill is described as are isolation and test procedures. Results indicate that plants did not show toxicity symptoms when exposed to BaP but did when grown in landfill soil. Some endophytes demonstrated plant growth-promotion capacity and tolerance to BaP and other organic compounds (diesel and PCB commercial mixtures). A few strains may even have the capacity to metabolize those organic pollutants. The overall decline in plant growth-promotion capacity in those strains isolated from the landfill soil experiment, compared with those from the bioassay with BaP, may indicate that lupin endophytes are not adapted to metal concentration in roots and shoots and fail to grow. As a result, most isolated root endophytes must have colonized root tissues from the soil. While preliminary degradation tests showed promising results (some strains exhibiting the potential to use organic pollutants as their sole source of carbon), these are not conclusive and further in-depth degradation assays need to be performed.

Profiling nematode communities in unmanaged flowerbed and agricultural field soils in Japan by DNA barcode sequencing

Soil nematodes play crucial roles in the soil food web and are a suitable indicator for assessing soil environments and ecosystems. Previous nematode community analyses based on nematode morphology classification have been shown to be useful for assessing various soil environments. Here we have conducted DNA barcode analysis for soil nematode community analyses in Japanese soils. We isolated nematodes from two different environmental soils of an unmanaged flowerbed and an agricultural field using the improved flotation-sieving method. Small subunit (SSU) rDNA fragments were directly amplified from each of 68 (flowerbed samples) and 48 (field samples) isolated nematodes to determine the nucleotide sequence. Sixteen and thirteen operational taxonomic units (OTUs) were obtained by multiple sequence alignment from the flowerbed and agricultural field nematodes, respectively. All 29 SSU rDNA-derived OTUs (rOTUs) were further mapped onto a phylogenetic tree with 107 known nematode species. Interestingly, the two nematode communities examined were clearly distinct from each other in terms of trophic groups: Animal predators and plant feeders were markedly abundant in the flowerbed soils, in contrast, bacterial feeders were dominantly observed in the agricultural field soils. The data from the flowerbed nematodes suggests a possible food web among two different trophic nematode groups and plants (weeds) in the closed soil environment. Finally, DNA sequences derived from the mitochondrial cytochrome oxidase c subunit 1 (COI) gene were determined as a DNA barcode from 43 agricultural field soil nematodes. These nematodes were assigned to 13 rDNA-derived OTUs, but in the COI gene analysis were assigned to 23 COI gene-derived OTUs (cOTUs), indicating that COI gene-based barcoding may provide higher taxonomic resolution than conventional SSU rDNA-barcoding in soil nematode community analysis.

Effects of soil mechanical resistance on nematode community structure under conventional sugarcane and remaining of Atlantic Forest

Nematodes present high potential as a biological indicator of soil quality. In this work, it was evaluated relations between soil physical properties and nematode community under sugarcane cropping and remaining of Atlantic Forest areas in Northeastern Pernambuco, Brazil. Soil samples were collected from September to November 2009 along two 200-m transects in both remaining of Atlantic Forest and sugarcane field at deeps of 0-10, 10-20, 20-30, 30-40, and 40-50 cm. For soil characterization, it was carried out analysis of soil size, water content, total porosity, bulk density, and particle density. The level of soil mechanical resistance was evaluated through a digital penetrometer. Nematodes were extracted per 300 cm(3) of soil through centrifugal flotation in sucrose being quantified, classified according trophic habit, and identified in level of genus or family. Data were analyzed using Pearson correlation at 5% of probability. Geostatistical analysis showed that the penetration resistance, water content, total porosity, and bulk density on both forest and cultivated area exhibited spatial dependence at the sampled scale, and their experimental semivariograms were fitted to spherical and exponential models. In forest area, the ectoparasites and free-living nematodes exhibited spherical model. In sugarcane field, the soil nematodes exhibited pure nugget effect. Pratylenchus sp. and Helicotylenchus sp. were prevalent in sugarcane field, but in forest, there was prevalence of Dorylaimidae and Rhabditidae. Total amount of nematode did not differ between environments; however, community trophic structure in forest presented prevalence of free-living nematodes: omnivores followed by bacterial-feeding soil nematodes, while plant-feeding nematodes were prevalent in sugarcane field. The nematode diversity was higher in the remaining of Atlantic Forest. However, the soil mechanical resistance was higher under sugarcane cropping, affecting more directly the free-living nematodes; especially Dorylaimidae which was the most sensible to changes in soil physical properties.

Heavy metals, salts and organic residues in old solid urban waste landfills and surface waters in their discharge areas: determinants for restoring their impact

This study was designed to determine the state of polluted soils in the main landfills of the Community of Madrid (central Spain), as part of a continuous assessment of the impacts of urban solid waste (USW) landfills that were capped with a layer of soil 20 years ago. Our analysis of this problem has been highly conditioned by the constant re-use of many of the USW landfills, since they have never been the target of any specific restoration plan. Our periodical analysis of cover soils and soils from discharge areas of the landfills indicates soil pollution has worsened over the years. Here, we examined heavy metal, salts, and organic compounds in soil and surface water samples taken from 15 landfills in the Madrid region. Impacts of the landfill soil covers on nematode and plant diversity were also evaluated. These analyses continue to reveal the presence of heavy metals (Zn, Cu, Cr, Ni, Pb, Cd) in soils, and salts (sulphates, chlorides and nitrates) in soils and surface waters. In addition, non-agricultural organic compounds, mainly aromatic and aliphatic hydrocarbons, often appeared in very high concentrations, and high levels of insecticides such as gamma-HCH (lindane) were also detected in soils. Around 50% of the water samples collected showed chemical demand of oxygen (CDO) values in excess of 150 mg/l. Traces of phenolic compounds were detected in some landfills, some of which exhibited high levels of 2-chlorophenol and pentachlorophenol. All these factors are conditioning both the revegetation of the landfill systems and the remediation of their slopes and terrestrial ecosystems arising in their discharge areas. This work updates the current situation and discusses risks for the health of the ecosystems, humans, domestic animals and wildlife living close to these landfills.

Ecotoxicological diagnosis of a sealed municipal landfill

Assessing the environmental impact of a soil-topped landfill requires an accurate ecotoxicological diagnosis. This paper describes various diagnostic protocols for this purpose and their application to a real case: the urban solid waste (USW) municipal landfill of Getafe (Madrid, Spain). After their initial sealing with soil from the surroundings about 20 years ago, most USW landfills in the autonomous community of Madrid have continued to receive waste. This has hindered precise assessment of their impact on their environment and affected ecosystems. The procedure proposed here overcomes this problem by assessing the situation in edaphic, aquatic and ecological terms. The present study focused on the most influential soil variables (viz. salinity due largely to the presence of anions, and heavy metals and organic compounds). These variables were also determined in surface waters of the wetland most strongly affected by leachates running down landfill slopes. Determinations included the characterization of plant communities and microbial biodiversity. The study was supplemented with a bioassay under controlled conditions in pots containing soil contaminated with variable concentrations of Zn (as ZnCl(2)) intended to assess ecochemical actions in a population of Bromus rubens, which grows profusely in the landfill.

Nematode community structure in the vicinity of a metallurgical factory

Soil nematode communities (taxa composition, trophic structure, ecological indices) in the area of metallurgical factory (Oravské ferozliatinárske závody) in Široká, Northern Slovakia were investigated in 2009. The factory belongs to main sources of emissions originated by ferroalloy production in this region. Four sites (meadows) were selected in a downwind direction from the factory: site A was located 0.85 km far from the factory, and the other sites were maintained in approximately 2-km intervals from each other. Chemical analysis of soil samples showed low concentrations of heavy metals (As, Cd, Cr, Cu, Ni, Pb and Zn), with all values being under Slovak limit concentrations of heavy metals in soils. Only the Cd content in the soil sample from site A slightly exceeded the allowable threshold, but it was decreasing with the distance from the factory, similarly as remaining metals except Cr, with slightly increasing trend of concentration. Within 64 identified nematode genera, the Helicotylenchus, Paratylenchus, Pratylenchus, Acrobeloides, Cephalobus and Rhabditis were most common and eudominant. This was clearly reflected on the trophic structure of nematode communities, where plant feeding nematodes and bacteriovorous prevailed. Significant negative correlation (P < 0.05) was observed between the abundance of bacteriovores and the concentration of Cu in the soil. On the other hand, fungivores showed significant correlation with Ni and Cr (P < 0.05) as well as predators with Cd, Pb and Zn contents in the soil (P < 0.01). The highly significant correlation (P < 0.05; P < 0.01) was found between As, Cd, Ni, Pb and Zn and Maturity Index 2-5. A negative relationship was detected between Maturity Index and the concentration of Cr in the soil (P < 0.01). On the other hand, Cu was in positive correlation with MI values. The MI, reflecting the degree of disturbances and changes in the structure and function of the soil ecosystem, was found to be the most sensitive indicator among all used indices.

Relationship between plant biodiversity and heavy metal bioavailability in grasslands overlying an abandoned mine

Abandoned metal mines in the Sierra de Guadarrama, Madrid, Spain, are often located in areas of high ecological value. This is true of an abandoned barium mine situated in the heart of a bird sanctuary. Today the area sustains grasslands, interspersed with oakwood formations of Quercus ilex and heywood scrub (Retama sphaerocarpa L.), used by cattle, sheep and wild animals. Our study was designed to establish a relationship between the plant biodiversity of these grasslands and the bioavailability of heavy metals in the topsoil layer of this abandoned mine. We conducted soil chemical analyses and performed a greenhouse evaluation of the effects of different soil heavy metal concentrations on biodiversity. The greenhouse bioassays were run for 6 months using soil samples obtained from the mine polluted with heavy metals (Cu, Zn, Pb and Cd) and from a control pasture. Soil heavy metal and Na concentrations, along with the pH, had intense negative effects on plant biodiversity, as determined through changes in the Shannon index and species richness. Numbers of grasses, legumes, and composites were reduced, whilst other species (including ruderals) were affected to a lesser extent. Zinc had the greatest effect on biodiversity, followed by Cd and Cu. When we compared the sensitivity of the biodiversity indicators to the different metal content variables, pseudototal metal concentrations determined by X-ray fluorescence (XRF) were the most sensitive, followed by available and soluble metal contents. Worse correlations between biodiversity variables and metal variables were shown by pseudototal contents obtained by plasma emission spectroscopy (ICP-OES). Our results highlight the importance of using as many different indicators as possible to reliably assess the response shown by plants to heavy metal soil pollution.

Nematode communities in contaminated river sediments

Nematode communities of eight sites from three river catchments were investigated in terms of the genera composition, feeding types, and life-history strategists. The sampling sites showed a gradient of anthropogenic contamination with heavy metals and organic pollutants being important factors in differentiating the sites. Nematode community structure was related to sediment pollution and the hydro-morphological structure of the sampling sites. Heavily contaminated sites were characterized by communities with high relative abundances of omnivorous and predacious nematodes (Tobrilus, c-p 3; Mononchus, c-p 4), while sites with low to medium contamination were dominated by bacterivorous nematodes (Monhystera, Daptonema; c-p 2) or suction feeders (Dorylaimus, c-p 4). The relatively high Maturity Index values in the heavily polluted sites were surprising. Nematodes turned out to be a suitable organism group for monitoring sediment quality, with generic composition being the most accurate indicator for assessing differences in nematode community structure.

Ecotoxicological assessment of the impact of residual heavy metals on soil nematodes in the Guadiamar River Basin (Southern Spain)

On 25 April 1998, as a consequence of the breaking of a dam containing the tailings of a pyrite mine, a land strip of approximately 43 km in length was covered with a layer of black sludge, containing high levels of heavy metals, along the Guadiamar River Basin (southern Spain). In this investigation we carried out an ecotoxicological assessment (field and laboratory studies) of the impact of residual heavy metals (Cu, Pb, Zn, Ni) on soil nematodes in the impacted riparian zone, two years after the huge mine spillage. Concentrations of residual heavy metals were significantly (P<0.05) higher at the impacted sampling sectors (S-2, S-3, S-4, S-5) than at the unpolluted (reference) sampling sector (S-1). Nickel however exhibited the lowest increases at the impacted sectors. As a consequence, correlation coefficients between concentrations of heavy metals and values of ecological indices were not significant for Ni. In contrast, copper, lead and zinc exhibited significant (P<0.05) negative correlation coefficients with ecological indices, particularly with diversity indices (including the~number of taxa). In addition, the toxicity of Cu and Pb to nematode test species (Aphelenchus avenae and Cephalobus persegnis) during short-term toxicity bioassays was much higher than the toxicity of Zn and Ni. We conclude that residual heavy metals were still influencing adversely the community of soil nematodes in the impacted riparian zone of the Guadiamar River Basin. Cu, Pb and, to a lesser extent, Zn would be major responsible for the observed impact.