What makes a better indicator? Taxonomic vs functional response of nematodes to estuarine gradient

Efficient implementation of nematodes-based indices for ecological quality assessment requires fundamental knowledge on their biodiversity and functional patterns along with the drivers that generate these patterns. Though, it is still unclear if nematodes taxonomical attributes are driven by the same environmental drivers as their functional (biological traits) counterparts, or if their taxonomical diversity is also enhanced by their functional diversity. To fill this knowledge gap, we investigated taxonomical (based on nematode genera abundances dataset) and functional attributes: trophic groups (TG) and life history strategies (LHS) of benthic nematodes collected from 35 sampling stations along the Sado Estuary, SW Portugal. Along with biological samples we measured environmental variables in the water and sediments as well as sediment grain size. Our results demonstrated that taxonomy-based assemblages were mainly structured by the salinity gradient and further by the interplay of granulometry and organic matter content. Contrastingly, trait-based distribution patterns were largely driven by the variations in the above sediment dissolved oxygen concentration. This finding largely draw attention to the role that above sediment dissolved oxygen concentration exerts on nematode assemblages and their functional distribution patterns. Consequently, our results demonstrate that biological traits introduce a new dimensionality in multivariate data that otherwise could not be detected using solely taxonomical information, thereby enhancing our knowledge on ecological gradients existing within an estuary. Additionally, we found a strong correlation between functional richness (based on the combination of TG and LHS traits) and diversity taxonomic metrics (species richness, Simpson and Shannon diversity), although no correlation was found between taxonomic diversity indices and single nematode ecological indices (ITD index of trophic diversity and MI Maturity Index). Therefore, the combined use of functional traits and its derived metrics was demonstrated to effectively reflect taxonomical diversity presenting reliable and highly complementary information for the assessment and monitoring of marine coastal sediments using benthic nematodes

Exploring the Use of Cytochrome Oxidase c Subunit 1 (COI) for DNA Barcoding of Free-Living Marine Nematodes

BackgroundThe identification of free-living marine nematodes is difficult because of the paucity of easily scorable diagnostic morphological characters. Consequently, molecular identification tools could solve this problem. Unfortunately, hitherto most of these tools relied on 18S rDNA and 28S rDNA sequences, which often lack sufficient resolution at the species level. In contrast, only a few mitochondrial COI data are available for free-living marine nematodes. Therefore, we investigate the amplification and sequencing success of two partitions of the COI gene, the M1-M6 barcoding region and the I3-M11 partition.MethodologyBoth partitions were analysed in 41 nematode species from a wide phylogenetic range. The taxon specific primers for the I3-M11 partition outperformed the universal M1-M6 primers in terms of amplification success (87.8% vs. 65.8%, respectively) and produced a higher number of bidirectional COI sequences (65.8% vs 39.0%, respectively). A threshold value of 5% K2P genetic divergence marked a clear DNA barcoding gap separating intra- and interspecific distances: 99.3% of all interspecific comparisons were >0.05, while 99.5% of all intraspecific comparisons were <0.05 K2P distance.ConclusionThe I3-M11 partition reliably identifies a wide range of marine nematodes, and our data show the need for a strict scrutiny of the obtained sequences, since contamination, nuclear pseudogenes and endosymbionts may confuse nematode species identification by COI sequence

Inconsistent impacts of decomposer diversity on the stability of aboveground and belowground ecosystem functions

The intensive discussion on the importance of biodiversity for the stability of essential processes in ecosystems has prompted a multitude of studies since the middle of the last century. Nevertheless, research has been extremely biased by focusing on the producer level, while studies on the impacts of decomposer diversity on the stability of ecosystem functions are lacking. Here, we investigate the impacts of decomposer diversity on the stability (reliability) of three important aboveground and belowground ecosystem functions: primary productivity (shoot and root biomass), litter decomposition, and herbivore infestation. For this, we analyzed the results of three laboratory experiments manipulating decomposer diversity (1–3 species) in comparison to decomposer-free treatments in terms of variability of the measured variables. Decomposer diversity often significantly but inconsistently affected the stability of all aboveground and belowground ecosystem functions investigated in the present study. While primary productivity was mainly destabilized, litter decomposition and aphid infestation were essentially stabilized by increasing decomposer diversity. However, impacts of decomposer diversity varied between plant community and fertility treatments. There was no general effect of the presence of decomposers on stability and no trend toward weaker effects in fertilized communities and legume communities. This indicates that impacts of decomposers are based on more than effects on nutrient availability. Although inconsistent impacts complicate the estimation of consequences of belowground diversity loss, underpinning mechanisms of the observed patterns are discussed. Impacts of decomposer diversity on the stability of essential ecosystem functions differed between plant communities of varying composition and fertility, implicating that human-induced changes of biodiversity and land-use management might have unpredictable effects on the processes mankind relies on. This study therefore points to the necessity of also considering soil feedback mechanisms in order to gain a comprehensive and holistic understanding of the impacts of current global change phenomena on the stability of essential ecosystem functions

Potential side effects of biocontrol and plant-growth promoting Bacillus amyloliquefaciens bacteria on earthworms

After 1-2 months, survival, growth and reproduction of the earthworms were recorded. We found no effect of the treatments as compared to control without BA amendments. We conclude that the use of high doses of BA with concentrations at the same magnitude as maximally expected when the bacteria are used as PGPR and BCA, is not harmful to the soil dwelling earthworms tested in this project. Further studies of the ecological effects of PGPR and BCA bacteria on other non-target soil organisms are encouraged. The development of sustainable agricultural systems, where ecosystem services are optimized, has to be aided by a deeper knowledge of the combined effect of bacteria and earthworms on the promotion of plant health. (C) 2015 Elsevier B.V. All rights reserved

Scientific Opinion addressing the state of the science on risk assessment of plant protection products for in-soil organisms

Following a request from EFSA, the Panel on Plant Protection Products and their Residues developed an opinion on the science behind the risk assessment of plant protection products for in-soil organisms. The current risk assessment scheme is reviewed, taking into account new regulatory frameworks and scientific developments. Proposals are made for specific protection goals for in-soil organisms being key drivers for relevant ecosystem services in agricultural landscapes such as nutrient cycling, soil structure, pest control and biodiversity. Considering the time-scales and biological processes related to the dispersal of the majority of in-soil organisms compared to terrestrial non-target arthropods living above soil, the Panel proposes that in-soil environmental risk assessments are made at in- and off-field scale considering field boundary levels. A new testing strategy which takes into account the relevant exposure routes for in-soil organisms and the potential direct and indirect effects is proposed. In order to address species recovery and long-term impacts of PPPs, the use of population models is also proposed

Soil biodiversity and nitrogen cycling under agricultural (de-)intensification

Bodemorganismen spelen een sleutelrol in de recycling van nutriënten door hun bijdrage aan de afbraak van organisch materiaal (decompositie), het beschikbaar maken van voedingstoffen (mineralisatie) die benut kunnen worden voor plantengroei en bioturbatie van de bodem. In de intensieve landbouw wordt deze rol ten dele overgenomen door het gebruik van kunstmest en grondbewerking. Deze landbouwpraktijken hebben het nadelige gevolg dat onder andere de diversiteit aan bodemorganismen afneemt, en nutrientenverliezen, met name stikstof, naar het milieu toenemen. Daarom hebben wetenschappers zich recentelijk in toenemende mate gericht op het creëren en ondersteunen van vormen van landbouw die op de lange termijn duurzaam zijn. Een efficiëntere benutting van nutrienten in agro-ecosystemen kan wellicht bereikt worden wanneer de bodemgemeenschap een grotere rol in de nutriëntencyclus gaat spelen