Daniel R. Lammel

Bio: Daniel R. Lammel is an academic researcher from Free University of Berlin. The author has contributed to research in topics: Soil biology & Ecosystem. The author has an hindex of 9, co-authored 16 publications receiving 457 citations. Previous affiliations of Daniel R. Lammel include University of Massachusetts Amherst & University of São Paulo.

Global distribution of earthworm diversity

Abstract: Soil organisms, including earthworms, are a key component of terrestrial ecosystems. However, little is known about their diversity, their distribution, and the threats affecting them. We compiled a global dataset of sampled earthworm communities from 6928 sites in 57 countries as a basis for predicting patterns in earthworm diversity, abundance, and biomass. We found that local species richness and abundance typically peaked at higher latitudes, displaying patterns opposite to those observed in aboveground organisms. However, high species dissimilarity across tropical locations may cause diversity across the entirety of the tropics to be higher than elsewhere. Climate variables were found to be more important in shaping earthworm communities than soil properties or habitat cover. These findings suggest that climate change may have serious implications for earthworm communities and for the functions they provide.

Why farmers should manage the arbuscular mycorrhizal symbiosis

Abstract: The Tansley review by Ryan & Graham (2018) provided a welcome critical perspective on the role of arbuscular mycorrhizal (AM) fungi in large‐scale industrial agriculture, with a focus on cereals (wheat, Triticum aestivum). They conclude that there is little evidence that farmers should consider the abundance or diversity of AM fungi when managing crops. We welcome many of the points made in the paper, as they give an opportunity for self‐reflection, considering that the importance of AM fungi in agroecosystems is often taken for granted. However, we suggest that it is too early to draw the overall conclusion that the management of AM fungi by farmers is currently not warranted. We offer the following points to contribute to the discussion. The first point pertains to the overall focus of Ryan & Graham (2018), which strongly determines the recommendations at which the authors arrive. This scope is limited to yield, at the expense of neglecting aspects of sustainability. We then argue that AM fungal communities do respond negatively to aspects of agricultural management, and list evidence for their positive effects to agronomically important traits, including yield in cereals. In our final argument, we advocate for transitioning to agroecosystems that are more AM compatible in order to increasingly take advantage of all the potential services these ancient symbionts, and other soil biota, can provide.

Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures.

Abstract: pH is frequently reported as the main driver for prokaryotic community structure in soils. However, pH changes are also linked to “spillover effects” on other chemical parameters (e.g., availability of Al, Fe, Mn, Zn, and Cu) and plant growth, but these indirect effects on the microbial communities are rarely investigated. Usually, pH also co-varies with some confounding factors, such as land use, soil management (e.g., tillage and chemical inputs), plant cover, and/or edapho-climatic conditions. So, a more comprehensive analysis of the direct and indirect effects of pH brings a better understanding of the mechanisms driving prokaryotic (archaeal and bacterial) community structures. We evaluated an agricultural soil pH gradient (from 4 to 6, the typical range for tropical farms), in a liming gradient with confounding factors minimized, investigating relationships between prokaryotic communities (16S rRNA) and physical–chemical parameters (indirect effects). Correlations, hierarchical modeling of species communities (HMSC), and random forest (RF) modeling indicated that both direct and indirect effects of the pH gradient affected the prokaryotic communities. Some OTUs were more affected by the pH changes (e.g., some Actinobacteria), while others were more affected by the indirect pH effects (e.g., some Proteobacteria). HMSC detected a phylogenetic signal related to the effects. Both HMSC and RF indicated that the main indirect effect was the pH changes on the availability of some elements (e.g., Al, Fe, and Cu), and secondarily, effects on plant growth and nutrient cycling also affected the OTUs. Additionally, we found that some of the OTUs that responded to pH also correlated with CO2, CH4, and N2O greenhouse gas fluxes. Our results indicate that there are two distinct pH-related mechanisms driving prokaryotic community structures, the direct effect and “spillover effects” of pH (indirect effects). Moreover, the indirect effects are highly relevant for some OTUs and consequently for the community structure; therefore, it is a mechanism that should be further investigated in microbial ecology.

Specific microbial gene abundances and soil parameters contribute to C, N, and greenhouse gas process rates after land use change in Southern Amazonian Soils

Abstract: Ecological processes regulating soil carbon (C) and nitrogen (N) cycles are still poorly understood, especially in the world's largest agricultural frontier in Southern Amazonia. We analyzed soil parameters in samples from pristine rainforest and after land use change to pasture and crop fields, and correlated them with abundance of functional and phylogenetic marker genes (amoA, nirK, nirS, norB, nosZ, nifH, mcrA, pmoA, and 16S/18S rRNA). Additionally, we integrated these parameters using path analysis and multiple regressions. Following forest removal, concentrations of soil C and N declined, and pH and nutrient levels increased, which influenced microbial abundances and biogeochemical processes. A seasonal trend was observed, suggesting that abundances of microbial groups were restored to near native levels after the dry winter fallow. Integration of the marker gene abundances with soil parameters using path analysis and multiple regressions provided good predictions of biogeochemical processes, such as the fluxes of NO3, N2O, CO2, and CH4. In the wet season, agricultural soil showed the highest abundance of nitrifiers (amoA) and Archaea, however, forest soils showed the highest abundances of denitrifiers (nirK, nosZ) and high N, which correlated with increased N2O emissions. Methanogens (mcrA) and methanotrophs (pmoA) were more abundant in forest soil, but methane flux was highest in pasture sites, which was related to soil compaction. Rather than analyzing direct correlations, the data integration using multivariate tools provided a better overview of biogeochemical processes. Overall, in the wet season, land use change from forest to agriculture reduced the abundance of different functional microbial groups related to the soil C and N cycles; integrating the gene abundance data and soil parameters provided a comprehensive overview of these interactions. Path analysis and multiple regressions addressed the need for more comprehensive approaches to improve our mechanistic understanding of biogeochemical cycles.

Global Multi-resolution Terrain Elevation Data 2010 (GMTED2010)

Abstract: For more information on the USGS—the Federal source for science about the Earth, its natural and living resources, natural hazards, and the environment, visit http://www.usgs.gov or call 1–888–ASK–USGS. For an overview of USGS information products, including maps, imagery, and publications, Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. Although this report is in the public domain, permission must be secured from the individual copyright owners to reproduce any copyrighted materials contained within this report. 10. Diagram showing the GMTED2010 layer extents (minimum and maximum latitude and longitude) are a result of the coordinate system inherited from the 1-arc-second SRTM

Arbuscular mycorrhizal fungi

Abstract: The potential disease suppressiveness of arbuscular mycorrhizal (AM) fungi of various origins on Bipolaris sorokiniana in barley has been investigated. Firstly, a survey considering the occurrence of AM fungi in arable fields in Sweden were conducted with the aim to exploit site specific genetic resources in relation to disease suppressiveness. Arbuscular mycorrhizal fungi were present at all 45 sampling sites surveyed all over Sweden at densities ranging from 3 up to 44 spores per gram air dried soil. The highest spore density was found in a semi-natural grassland and the lowest were found in a cereal monoculture. The AM fungi were then multiplied in trap cultures in the greenhouse with the aim to use these for studying potential disease suppressiveness. Thus, the effects of the AM fungi trap cultures on the transmission of seed-borne B. sorokiniana in barley were investigated, using the trap culture inocula, but also including inocula consisting on spore mixtures. The arbuscular mycorrhizal fungi were able to suppress the transmission of B. sorokiniana in aerial parts of barley plants. The degree of suppression varied with the origin of the AM fungal trap cultures. The trap culture inoculum with the highest suppression of the B. sorokiniana transmission originated from an organically managed barley field with undersown ley. The two spore-inocula with the best suppression of the pathogen originated from fields with winter wheat and spring barley, respectively. Eventually, an in vitro method was developed for studying the effect of AM fungal colonisation of roots on the development of foliar diseases and the reaction of the actual host plant of the disease causing organism. Using the developed method, it was indicated that AM fungal colonisation of barley plant suppressed the development of leaf necroses due to B. sorokiniana. Further in vitro studies on the interaction between B. sorokiniana and arbuscular mycorrhizal fungi showed that B. sorokiniana decrease the germination of the AM fungal spores. In conclusion, AM fungi suppress the development of B. sorokiniana in barley. My data suggest that for biocontrol of B. sorokiniana AM fungi should be considered.

AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential.

Abstract: Understanding the evolutionary background of a bacterial isolate has applications for a wide range of research. However generating an accurate species phylogeny remains challenging. Reliance on 16S rDNA for species identification currently remains popular. Unfortunately, this widespread method suffers from low resolution at the species level due to high sequence conservation. Currently, there is now a wealth of genomic data that can be used to yield more accurate species designations via modern phylogenetic methods and multiple genetic loci. However, these often require extensive expertise and time. The Automated Multi-Locus Species Tree (autoMLST) was thus developed to provide a rapid ‘one-click’ pipeline to simplify this workflow at: https://automlst.ziemertlab.com. This server utilizes Multi-Locus Sequence Analysis (MLSA) to produce high-resolution species trees; this does not preform multi-locus sequence typing (MLST), a related classification method. The resulting phylogenetic tree also includes helpful annotations, such as species clade designations and secondary metabolite counts to aid natural product prospecting. Distinct from currently available web-interfaces, autoMLST can automate selection of reference genomes and out-group organisms based on one or more query genomes. This enables a wide range of researchers to perform rigorous phylogenetic analyses more rapidly compared to manual MLSA workflows.

Ecology of Nitrogen Fixing, Nitrifying, and Denitrifying Microorganisms in Tropical Forest Soils.

Abstract: Soil microorganisms play important roles in nitrogen cycling within forest ecosystems. Current research has revealed that a wider variety of microorganisms, with unexpected diversity in their functions and phylogenies, are involved in the nitrogen cycle than previously thought, including nitrogen-fixing bacteria, ammonia-oxidizing bacteria and archaea, heterotrophic nitrifying microorganisms, and anammox bacteria, as well as denitrifying bacteria, archaea, and fungi. However, the vast majority of this research has been focused in temperate regions, and relatively little is known regarding the ecology of nitrogen-cycling microorganisms within tropical and subtropical ecosystems. Tropical forests are characterized by relatively high precipitation, low annual temperature fluctuation, high heterogeneity in plant diversity, large amounts of plant litter, and unique soil chemistry. For these reasons, regulation of the nitrogen cycle in tropical forests may be very different from that of temperate ecosystems. This is of great importance because of growing concerns regarding the effect of land use change and chronic-elevated nitrogen deposition on nitrogen-cycling processes in tropical forests. In the context of global change, it is crucial to understand how environmental factors and land use changes in tropical ecosystems influence the composition, abundance and activity of key players in the nitrogen cycle. In this review, we synthesize the limited currently available information regarding the microbial communities involved in nitrogen fixation, nitrification and denitrification, to provide deeper insight into the mechanisms regulating nitrogen cycling in tropical forest ecosystems. We also highlight the large gaps in our understanding of microbially mediated nitrogen processes in tropical forest soils and identify important areas for future research.