scholarly journals Invasive Earthworms Alter Forest Soil Microbiomes and Nitrogen Cycling

2021 ◽  
Author(s):  
Jeonghwan Jang ◽  
Xianyi Xiong ◽  
Chang Liu ◽  
Kyungsoo Yoo ◽  
Satoshi Ishii
Keyword(s):  
Nitrogen Cycling ◽  
Soil Depth ◽  
Amplicon Sequencing ◽  
Biological Properties ◽  
Northern Hardwood Forests ◽  
Shotgun Metagenomics ◽  
Earthworm Invasion ◽  
Invasive Earthworms ◽  
Exotic Earthworms ◽  
Different Depths

AbstractNorthern hardwood forests in formerly glaciated areas had been free of earthworms until exotic European earthworms were introduced by human activities. The invasion of exotic earthworms is known to dramatically alter soil physical, geochemical, and biological properties, but its impacts on soil microbiomes are still unclear. Here we show that the invasive earthworms alter soil microbiomes and ecosystem functioning, especially for nitrogen cycling. We collected soil samples at different depths from three sites across an active earthworm invasion chronosequence in a hardwood forest in Minnesota, USA. We analyzed the structures and the functional potentials of the soil microbiomes by using amplicon sequencing, high-throughput nitrogen cycle gene quantification (NiCE chip), and shotgun metagenomics. Both the levels of earthworm invasion and soil depth influenced the microbiome structures. In the most recently and minimally invaded soils, Nitrososphaera and Nitrospira as well as the genes related to nitrification were more abundant than in the heavily invaded soils. By contrast, genes related to denitrification and nitrogen fixation were more abundant in the heavily invaded than the minimally invaded soils. Our results suggest that the N cycling in forest soils is mostly nitrification driven before earthworm invasion, whereas it becomes denitrification driven after earthworm invasion.

LYSIMETERS WITH RAINFALL AND SOIL WATER CONTROL

1971 ◽  
Vol 2 (2) ◽  
pp. 79-92 ◽  
Author(s):  
K. J. KRISTENSEN ◽  
H. C. ASLYNG
Keyword(s):  
Soil Moisture Content ◽  
Soil Depth ◽  
Irrigation System ◽  
Drainage System ◽  
Soil Surface ◽  
Trickle Irrigation ◽  
Water Control ◽  
Radiation Equipment ◽  
Different Depths ◽  
Growth Experiments

The lysimeter installation described comprises 36 concrete tanks each with a soil surface of 4 m2. The installation is useful for plant growth experiments under natural conditions involving different treatment combined with various controlled water supplies. The ground installation is at least 20 cm below the soil surface and tillage can be done with field implements. The lysimeter tanks are provided with a drainage system which can drain the soil at the bottom (100 cm depth) to a tension of up to 100 cm. A constant ground-water table at less than 100 cm soil depth can also be maintained. The soil moisture content at different depths is determined from an underground tunnel by use of gamma radiation equipment in metal tubes horizontally installed in the soil. Rainfall is prevented by a movable glass roof automatically operated and controlled by a special rain sensor. Water is applied to the soil surface with a special trickle irrigation system consisting of a set of plastic tubes for each lysimeter tank and controlled from the tunnel. Fertilizers in controlled amount can be applied with the irrigation water.

scholarly journals Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kazutoshi Yoshitake ◽  
Gaku Kimura ◽  
Tomoko Sakami ◽  
Tsuyoshi Watanabe ◽  
Yukiko Taniuchi ◽  
...  
Keyword(s):  
Time Series ◽  
Microbial Communities ◽  
Pacific Coast ◽  
Three Dimensional ◽  
Amplicon Sequencing ◽  
Metagenomic Data ◽  
Shotgun Metagenomics ◽  
Functional Features ◽  
Pacific Coast Of Japan ◽  
Marine Microbial Communities

AbstractAlthough numerous metagenome, amplicon sequencing-based studies have been conducted to date to characterize marine microbial communities, relatively few have employed full metagenome shotgun sequencing to obtain a broader picture of the functional features of these marine microbial communities. Moreover, most of these studies only performed sporadic sampling, which is insufficient to understand an ecosystem comprehensively. In this study, we regularly conducted seawater sampling along the northeastern Pacific coast of Japan between March 2012 and May 2016. We collected 213 seawater samples and prepared size-based fractions to generate 454 subsets of samples for shotgun metagenome sequencing and analysis. We also determined the sequences of 16S rRNA (n = 111) and 18S rRNA (n = 47) gene amplicons from smaller sample subsets. We thereafter developed the Ocean Monitoring Database for time-series metagenomic data (http://marine-meta.healthscience.sci.waseda.ac.jp/omd/), which provides a three-dimensional bird’s-eye view of the data. This database includes results of digital DNA chip analysis, a novel method for estimating ocean characteristics such as water temperature from metagenomic data. Furthermore, we developed a novel classification method that includes more information about viruses than that acquired using BLAST. We further report the discovery of a large number of previously overlooked (TAG)n repeat sequences in the genomes of marine microbes. We predict that the availability of this time-series database will lead to major discoveries in marine microbiome research.

scholarly journals Reduced metagenome sequencing for strain-resolution taxonomic profiles

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Lars Snipen ◽  
Inga-Leena Angell ◽  
Torbjørn Rognes ◽  
Knut Rudi
Keyword(s):  
Microbial Community ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
Good Alternative ◽  
Shotgun Sequencing ◽  
Least Square ◽  
Full Potential ◽  
Shotgun Metagenomics ◽  
Metagenome Sequencing ◽  
Reference Genomes

Abstract Background Studies of shifts in microbial community composition has many applications. For studies at species or subspecies levels, the 16S amplicon sequencing lacks resolution and is often replaced by full shotgun sequencing. Due to higher costs, this restricts the number of samples sequenced. As an alternative to a full shotgun sequencing we have investigated the use of Reduced Metagenome Sequencing (RMS) to estimate the composition of a microbial community. This involves the use of double-digested restriction-associated DNA sequencing, which means only a smaller fraction of the genomes are sequenced. The read sets obtained by this approach have properties different from both amplicon and shotgun data, and analysis pipelines for both can either not be used at all or not explore the full potential of RMS data. Results We suggest a procedure for analyzing such data, based on fragment clustering and the use of a constrained ordinary least square de-convolution for estimating the relative abundance of all community members. Mock community datasets show the potential to clearly separate strains even when the 16S is 100% identical, and genome-wide differences is < 0.02, indicating RMS has a very high resolution. From a simulation study, we compare RMS to shotgun sequencing and show that we get improved abundance estimates when the community has many very closely related genomes. From a real dataset of infant guts, we show that RMS is capable of detecting a strain diversity gradient for Escherichia coli across time. Conclusion We find that RMS is a good alternative to either metabarcoding or shotgun sequencing when it comes to resolving microbial communities at the strain level. Like shotgun metagenomics, it requires a good database of reference genomes and is well suited for studies of the human gut or other communities where many reference genomes exist. A data analysis pipeline is offered, as an R package at https://github.com/larssnip/microRMS.

scholarly journals Earthworms as an Ecological Indicator of Soil Recovery after Mechanized Logging Operations in Mixed Beech Forests

Forests ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 18
Author(s):  
Hadi Sohrabi ◽  
Meghdad Jourgholami ◽  
Mohammad Jafari ◽  
Farzam Tavankar ◽  
Rachele Venanzi ◽  
...  
Keyword(s):  
Soil Properties ◽  
Soil Depth ◽  
Biological Properties ◽  
Economic Benefits ◽  
Ecological Indicator ◽  
Traffic Intensity ◽  
Soil Biological Properties ◽  
Density And Biomass ◽  
Soil Recovery ◽  
The Impact

Soil damage caused by logging operations conducted to obtain and maximize economic benefits has been established as having long-term effects on forest soil quality and productivity. However, a comprehensive study of the impact of logging operations on earthworms as a criterion for soil recovery has never been conducted in the Hyrcanian forests of Iran. The aim of this study was to determine the changes in soil biological properties (earthworm density and biomass) and its recovery process under the influence of traffic intensity, slope and soil depth in various intervals according to age after logging operations. Soil properties were compared among abandoned skid trails with different ages (i.e., 3, 10, 20, and 25 years) and an undisturbed area. The results showed that earthworm density and biomass in the high traffic intensity and slope class of 20–30% at the 10–20 cm depth of the soil had the lowest value compared to the other treatments. Twenty-five years after the logging operations, the earthworm density at soil depth of 0–10 and 10–20 cm was 28.4% (0.48 ind. m−2) and 38.6% (0.35 ind. m−2), which were less than those of the undisturbed area, respectively. Meanwhile, the earthworm biomass at a soil depth of 0–10 and 10–20 cm was 30.5% (2.05 mg m−2) and 40.5% (1.54 mg m−2) less than the values of the undisturbed area, respectively. The earthworm density and biomass were positively correlated with total porosity, organic carbon and nitrogen content, while negatively correlated with soil bulk density and C/N ratio. According to the results, 25 years after logging operations, the earthworm density and biomass on the skid trails were recovered, but they were significantly different with the undisturbed area. Therefore, full recovery of soil biological properties (i.e., earthworm density and biomass) takes more than 25 years. The conclusions of our study reveal that the effects of logging operations on soil properties are of great significance, and our understanding of the mechanism of soil change and recovery demand that harvesting operations be extensively and properly implemented.

scholarly journals Aboveground impacts of a belowground invader: how invasive earthworms alter aboveground arthropod communities in a northern North American forest

2021 ◽  
Author(s):  
Malte Jochum ◽  
Lise Thouvenot ◽  
Olga Ferlian ◽  
Romy Zeiss ◽  
Bernhard Klarner ◽  
...  
Keyword(s):  
Species Richness ◽  
Structural Equation ◽  
Structural Equation Models ◽  
Trophic Levels ◽  
Arthropod Community ◽  
Arthropod Communities ◽  
Earthworm Invasion ◽  
Invasive Earthworms ◽  
Invasion Impacts ◽  
Arthropod Abundance

AbstractDeclining arthropod communities have recently gained a lot of attention with climate and land-use change among the most-frequently discussed drivers. Here, we focus on a seemingly underrepresented driver of arthropod-community decline: biological invasions. For ∼12,000 years, earthworms have been absent from wide parts of northern North America, but they have been re-introduced with dramatic consequences. Most studies investigating earthworm-invasion impacts focus on the belowground world, resulting in limited knowledge on aboveground-community changes. We present observational data on earthworm, plant, and aboveground-arthropod communities in 60 plots, distributed across areas with increasing invasion status (low, medium, high) in a Canadian forest. We analyzed how earthworm-invasion status and biomass impact aboveground arthropod community abundance, biomass, and species richness, and how earthworm impacts cascade across trophic levels. We sampled ∼13,000 arthropods, dominated by Hemiptera, Diptera, Araneae, Thysanoptera, and Hymenoptera. Total arthropod abundance, biomass, and species richness declined significantly from areas of low to those with high invasion status with reductions of 61, 27, and 18%, respectively. Structural Equation Models unraveled that earthworms directly and indirectly impact arthropods across trophic levels. We show that earthworm invasion can alter aboveground multitrophic arthropod communities and suggest that belowground invasions can be important drivers of aboveground-arthropod decline.

scholarly journals Soil Temperature Estimation with Meteorological Parameters by Using Tree-Based Hybrid Data Mining Models

Mathematics ◽  
2020 ◽  
Vol 8 (9) ◽  
pp. 1407
Author(s):  
Mohammad Taghi Sattari ◽  
Anca Avram ◽  
Halit Apaydin ◽  
Oliviu Matei
Keyword(s):  
Soil Temperature ◽  
Soil Depth ◽  
Sunshine Duration ◽  
Evaluation Criteria ◽  
Nonlinear Problems ◽  
Soil Temperatures ◽  
Different Depths ◽  
Windowing Technique ◽  
Using Data ◽  
Research Decision

The temperature of the soil at different depths is one of the most important factors used in different disciplines, such as hydrology, soil science, civil engineering, construction, geotechnology, ecology, meteorology, agriculture, and environmental studies. In addition to physical and spatial variables, meteorological elements are also effective in changing soil temperatures at different depths. The use of machine-learning models is increasing day by day in many complex and nonlinear branches of science. These data-driven models seek solutions to complex and nonlinear problems using data observed in the past. In this research, decision tree (DT), gradient boosted trees (GBT), and hybrid DT–GBT models were used to estimate soil temperature. The soil temperatures at 5, 10, and 20 cm depths were estimated using the daily minimum, maximum, and mean temperature; sunshine intensity and duration, and precipitation data measured between 1993 and 2018 at Divrigi station in Sivas province in Turkey. To predict the soil temperature at different depths, the time windowing technique was used on the input data. According to the results, hybrid DT–GBT, GBT, and DT methods estimated the soil temperature at 5 cm depth the most successfully, respectively. However, the best estimate was obtained with the DT model at soil depths of 10 and 20 cm. According to the results of the research, the accuracy rate of the models has also increased with increasing soil depth. In the prediction of soil temperature, sunshine duration and air temperature were determined as the most important factors and precipitation was the most insignificant meteorological variable. According to the evaluation criteria, such as Nash-Sutcliffe coefficient, R, MAE, RMSE, and Taylor diagrams used, it is recommended that all three (DT, GBT, and hybrid DT–GBT) data-based models can be used for predicting soil temperature.

The effects of replaced topsoil of different depths on the vegetation and soil properties of reclaimed coal mine spoils in an alpine mining area

2019 ◽  
Vol 65 (3-4) ◽  
pp. 92-105
Author(s):  
Xinguang Yang ◽  
Xilai Li ◽  
Mingming Shi ◽  
Liqun Jin ◽  
Huafang Sun
Keyword(s):  
Plant Growth ◽  
Soil Properties ◽  
Coal Mine ◽  
Growth Parameters ◽  
Soil Depth ◽  
Mining Area ◽  
Vegetation Coverage ◽  
Mine Spoils ◽  
Plant Soil ◽  
Different Depths

Replacement of topsoil to an appropriate depth is one of the key methods for ecological restoration. The objective of this study was to investigate the effects of topsoil replacement depth on vegetation and soil properties, and to identify the optimum soil depth for reclamation of coal mine spoils in a cold alpine mining area. We sowed 3 herbaceous species after coal mine spoil heaps were treated with topsoil to 3 depths (0, 20‒25, 40‒45 cm). The variations in vegetation community structure, plant growth, soil properties were measured at different replaced topsoil depths. The correlations between plant and soil properties were analyzed statistically. The results showed species richness, diversity and evenness were not significantly different among different depths of topsoil (P > 0.05). Vegetation coverage, density, height and aboveground biomass increased significantly (P < 0.05) with increasing topsoil depth. Soil properties did not change significantly with increasing topsoil depth (P > 0.05), but soil organic matter was significantly higher at 40‒45 cm topsoil depth than at other two depths (P < 0.05). All soil properties, with the exception of total potassium, were positively correlated with the plant growth parameters. The 40‒45 cm topsoil depth of replacement should be considered as effective method in reclaiming coal mine spoils. The use of both topsoil replacement to a depth of 40‒45 cm and sowing of suitable herbaceous seeds is found to be an effective restoration strategy. Additionally, fertilization might be used as a substitute for artificial topsoil replacement to improve soil quality and speed up revegetation process by the positive plant-soil interactions.

scholarly journals Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Kirsten A. Ziesemer ◽  
Allison E. Mann ◽  
Krithivasan Sankaranarayanan ◽  
Hannes Schroeder ◽  
Andrew T. Ozga ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Amplification ◽  
Amplicon Sequencing ◽  
Universal Primers ◽  
Rrna Gene ◽  
Dental Calculus ◽  
Shotgun Metagenomics ◽  
Variable Regions ◽  
V3 Region

Abstract To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341–534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.

Influence of 10 years of conservation tillage on some biological properties of a fine sandy loam in the potato phase of two crop rotations in Atlantic Canada

2009 ◽  
Vol 89 (4) ◽  
pp. 391-402 ◽  
Author(s):  
M R Carter ◽  
R D Peters ◽  
C Noronha ◽  
J Kimpinski
Keyword(s):  
Sandy Loam ◽  
Conservation Tillage ◽  
Soil Depth ◽  
Conventional Tillage ◽  
Biological Properties ◽  
Soil Organic C ◽  
Tillage Practice ◽  
Organic C ◽  
Fine Sandy Loam ◽  
Potato Rotation

Conservation practices in potato (Solanum tuberosum L.) cropping systems can reduce excess tillage, provide crop residue cover, and maintain crop productivity; however, little is known about their long-term influence on soil biota and biological properties. Conservation tillage was evaluated in two potato rotations: a 2-yr barley-potato rotation and 3-yr clover-based (barley-red clover-potato) rotation initiated in 1994 on a fine sandy loam (Orthic Podzol) in Prince Edward Island, eastern Canada. Soil samples were obtained in 2003 from the 0- to 10-cm soil depth of the potato phase of both rotations to evaluate the influence of conservation, compared with conventional tillage, on changes in soil fertility, soil structural properties, soil C and N fractions, soil-borne pathogens, nematode communities, and micro-arthropod (Collembola and Acari) communities. The 3-yr conservation tillage practice improved soil structural stability, increased soil extractable P and K, increased soil organic C and total N and their particulate fractions, compared with the other treatments. Comparisons with earlier studies indicated that soil organic C had reached an equilibrium level at the 0- to 10-cm soil depth. Reduction of potato disease caused by Rhizoctonia solani was evident in the 3-yr rotation, compared with the 2-yr rotation, but was not influenced by tillage practice. Plant parasitic nematodes were not greatly influenced by rotation and tillage treatments; however, densities of the beneficial bacterial-feeding nematodes were increased under the 3-yr conservation tillage treatment. The abundance of micro-arthropods was increased by conservation tillage, while their diversity was mainly influenced by the rotation cycle rather than tillage practice. Overall, the 3-yr conservation tillage treatment provided a more beneficial soil biological condition than the other treatments, especially when compared with the 2-yr conventional tillage practice. Key words: Conservation systems, potato rotation, fine sandy loam, soil fertility, soil organic C and N fractions, soil structure, soil-borne pathogens, nematode, Collembola; Acari

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