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openmit-licenseOct 2024View details →

Code and Data for Manuscript "How raw milk-based adjunct cultures influence the microbial diversity in cheese"

This repository contains the data and code used in the study "How raw milk-based adjunct cultures influence the microbial diversity in cheese" by Dreier et al. (2024). The study investigates the impact of raw milk-based adjunct cultures (NMAC) on the microbial diversity of cheese. The data includes 16S rRNA gene amplicon sequences from cheese samples, as well as metadata and code used for data analysis.

opencc-by-4.0Mar 2022View details →

Salt flat microbial diversity and population structure along a salinity gradient

In this study, we examined the abundance of microbial communities in coastal sabkha and sabkha-shore regions in Abu Dhabi, UAE using 16s rDNA, and performed whole-genome metagenome analysis to elucidate the genetic heterogeneity of microbial species. Based on the 16s rDNA based prokaryotic microbial profile, we identified unusual coastal sabkha-specific microbial communities, consistent with the whole genome metagenome analysis. Out of 225 assembled microbial metagenomes, we analyzed 82 of the most abundant assembled genomes at the order and class taxonomic levels. We observed diversity was higher for some microbial populations on the inner regions of the sabkha as well as outside it, although the overall population diversity was higher within the sabkha. Our results show genetic structure over local spatial scales, different level of homologous recombination for different species as well as gene-specific selective sweeps. These results pave the way to understanding the ecological roles, salt stress tolerance mechanisms, and potential applications of sabkha microbial genes.

opencc-by-4.0Apr 2022View details →

Microbial diversity in streams draining proglacial floodplains

This dataset contains X files:  16S rRNA data: <ul> <li>16S_table.csv: Absolute abundance for each ASV. Absolute abundance were obtaines by using the relative abundance form read count and multiply it by the bacterial abundance measured through flowcytometer. ASV are rows and samples are columns. </li> <li>16S_Taxonomy.csv: The taxonomy obtained for each ASV. </li> <li>16S_Metadata.csv: Information on the samples ( Glacier, date, longitude, latitude, stream type,...) </li> </ul> 18S rRNA data:  <ul> <li>18S_otu_table.csv: Read count for each OTU. 18S ASVs were clustered into operational taxonomic units (OTUs) using a 97% identity threshold using the vsearch de novo clustering method implemented in qiime2.</li> <li>18S_Taxonomy_NEW.csv: The taxonomy obtained for each OTU, updated with SILVA update in October 2021. </li> <li>18S_Metadata: Information on the samples ( Glacier, date, longitude, latitude, stream type,...) </li> </ul> Water physiochemical parameter  <ul> <li>water_data.csv : [DOC, Na+, Mg2+, K, Ca2+, Cl-, SO42-,NH3, NOx, PO4, NO2, SRP, Alkalinity] are in ppb (mg/L)  [Temp] (Temperature) is in °C [Conductivity] is in uS/cm  [Turbidity] is in NTU  dD_H: water stable isotope of deuterium d18_16: water stable isotope Oxygen </li> </ul> Sediment biomass data <ul> <li>Biomass_data.csv:  Chla (chlorophyll-a concentration) is in ug Chla / g of DM (dry mass)  Bacterial_abundance: Number of bacteria counted by flow cytometer  BCP: Bacterial carbon production is in ng C g-1DM h-1 EPS: Extracelluar Polymeric substance is in glucose-equivalent g-1DM</li> </ul> Co-occurnece Network anaylsis - all file are in a subfolder /Network <ul> <li>Raw files to be pre-process :  <ul> <li>GFS_Fungi_links.csv, GFS_Fungi_nodes.csv, Trib_Fungi_links.csv, Trib_Fungi_nodes.csv</li> </ul> </li> <li>Pre-processed file used for plotting: <ul> <li>GFS_links_edit.csv, GFS_node_edit.csv, Trib_links_edit.csv, Trib_node_edit.csv,  </li> </ul> </li> </ul>

opencc-zeroApr 2022View details →

Dataset for manuscript entitled: Switchgrass cropping systems affect soil carbon and nitrogen and microbial diversity and activity on marginal lands

Switchgrass (Panicum virgatum L.), as a dedicated bioenergy crop, can provide cellulosic feedstock for biofuel production while improving or maintaining soil quality. However, comprehensive evaluations of how switchgrass cultivation and nitrogen (N) management impact soil and plant parameters remain incomplete. We conducted field trials in three years (2016–2018) at six locations in the North Central Great Lakes Region to evaluate the effects of cropping systems (switchgrass, restored prairie, undisturbed control) and N rates (0, 56 kg N ha-1 yr-1) on biomass yield and soil physicochemical, microbial, and enzymatic parameters. Switchgrass cropping system yielded an aboveground biomass 2.9–3.3 times higher than the other two systems (Jayawardena et al., In submission) but our study found that this biomass accumulation didn't reduce soil dissolved organic C (DOC), total dissolved N (TDN), or bacterial diversity. The annual aboveground biomass removal for bioenergy feedstock, however, reduced soil microbial biomass C (MBC) and N (MBN) and bacterial richness in the 2nd and 3rd years; despite this, continuous monocropping of switchgrass improved soil TDN, inorganic N, bacterial diversity, and shoot biomass in the 2nd and/or 3rd years when compared to the 1st year. N fertilization increased aboveground biomass yield by 1.2 times and significantly increased soil TDN, MBN, and the shoot biomass of switchgrass when compared to the unfertilized control. Locations with higher C and N contents and lower C:N ratio had higher aboveground biomass, MBC, MBN, and the activity of BG, CBH, and UREA enzymes; by contrast, locations with higher pH had higher soil TDN and activity of NAG and LAP enzymes. Our research demonstrates that switchgrass cultivation could improve or maintain soil N content and N fertilization can increase plant biomass yield. The comprehensive data also can inform future biogeochemical models to successfully implement switchgrass for bioenergy production.

opencc-zeroDec 2021View details →

Soil microbial diversity and community composition during conversion from conventional to organic agriculture

It is generally assumed that the dependence of conventional agriculture on artificial fertilizers and pesticides strongly impacts the environment, while organic agriculture relying more on microbial functioning may mitigate these impacts. However, it is not well known how microbial diversity and community composition change in conventionally managed farmers' fields that are converted to organic management. Here, we sequenced bacterial and fungal communities of 34 organic fields on sand and marine clay soils in a time series (chronosequence) covering 25 years of conversion. Nearby conventional fields were used as references. We found that community composition of bacteria and fungi differed between organic and conventionally managed fields. In the organic fields, fungal diversity increased with time since conversion. However, this effect disappeared when the conventional paired fields were included. There was a relationship between pH and soil organic matter content and the diversity and community composition of bacteria and fungi. In marine clay soils, when time since organic management increased, fungal communities in organic fields became more dissimilar to those in conventional fields. We conclude that conversion to organic management in these Dutch farmers' fields did not increase microbial community diversity. Instead, we observed that in organic fields in marine clay when time since conversion increased soil fungal community composition became progressively dissimilar from that in conventional fields. Our results also showed that the paired sampling approach of organic and conventional fields was essential in order to control for environmental variation that was otherwise unaccounted for.

opencc-by-4.0Feb 2017View details →

Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta)

This data depository contains analysis results from Parks, Wickett, and Alverson 2017 (Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta) (Mol. Biol. Evol. doi:10.1093/molbev/msx268)), and is made freely available to the research community. The file and subfolders here are as follows: gene_alignments - contains compressed (tarred and gzipped) folders with all gene alignments at 0.2, 0.5 and 0.8 alignment column occupancy cutoffs. In each folder, there are also text files listing which gene alignments fall under which taxon occupancy subsetting strategy (i.e., 10-20% taxon occupancy, 40-60% taxon occupancy, 80-100% taxon occupancy, etc). gene_trees - contains all (compressed) gene trees (bootstrapped versions, 100 bootstrap pseudo-replicates)) used in Astral analyses for each alignment column occupancy cutoff (0.2, 0.5, 0.8); nodes with less than 33% bootstrap support are collapsed. hmms.mafft_aligned - contains (compressed) hmm specifications for each major diatom morphotype (radial and polar centrics, araphid and raphid pennates) from the 0.2 alignment column occupancy subset of the data. A summary of the sampling scheme and the hmm results/counts are also available in HMM_sampling.docx. mmetsp_nuclear_transcriptome_assemblies - these are the compressed nuclear transcriptome assemblies that were done in-house (i.e., mostly MMETSP samples). Assemblies do not include organellar or rDNA loci. species_trees - contains (compressed) species trees for all phylogenetic strategies and alignment column occupancy cutoff/data subset strategies. Suppl_1.MMETSP_basic_summaries.xlsx - this an identical file to Parks, Wickett and Alverson 2017 supplementary file 1. This file contains taxon, strain and SRA information for all assembled taxa, and a variety of assembly metric information.

opencc-by-4.0Dec 2023View details →

Figure 8 in Microbial diversity of ticks and a novel typhus group Rickettsia species (Rickettsiales bacterium Ac37b) in Inner Mongolia, China

Figure 8. The composition of bacteria and pathogenic bacteria with a high abundance.

opencc-zeroJun 2024View details →

Climate regulates the effect of land-use change on the diversity of soil microbial functional groups and soil multifunctionality

Although studies have explored how soil microbial diversity and soil multifunctionality respond to land-use change at local scales, they have rarely been explored at larger scales and across different climatic and soil environmental conditions. By sampling 40 paired sites of land-use change from natural forests to agricultural lands (including croplands and orchards) along the middle and lower Yangtze River, combined with a global meta-analysis, we investigated the effects of land-use change and climate on the alpha and beta diversity of soil bacterial and fungal functional groups (FGs) and their associated soil multifunctionality at a regional scale. Our results showed that land-use change strongly changed the diversity of soil bacterial and fungal FGs and decreased multifunctionality, which was supported by our meta-analysis at a global scale. Direct effects of land-use change and climate and their interaction, together with changes in soil environmental variables, were the main determinants of the land-use change-induced changes in the diversity of soil bacterial or fungal FGs. The land-use change-induced decrease in multifunctionality was mainly associated with the direct effect of forest conversion, soil fertility, and diversity of fungal FGs. Furthermore, climate also regulated the effects of land-use change on multifunctionality by affecting soil fertility and fungal FGs diversity along the Yangtze River. Synthesis and applications. Taken together, our findings highlight the important effects of land-use change, climate, and their interactions on microbial diversity and multifunctionality, and suggest that effective land-use management and climate change mitigation strategies should be adopted to protect biodiversity and ecosystem function in the Yangtze River Basin.

Figure 1 in Analysis of microbial diversity in the root of Astragalus mongholicus

Figure 1. Photos of the NS and SS samples.

Figure 3 in Analysis of microbial diversity in the root of Astragalus mongholicus

Figure 3. Rarefaction curve of the NS and SS samples.

Figure 2 in Analysis of microbial diversity in the root of Astragalus mongholicus

Figure 2. OTU Venn diagram of the NS and SS samples.

Figure 4 in Analysis of microbial diversity in the root of Astragalus mongholicus

Figure 4. Species richness at the class level.

opencc-by-4.0Dec 2023View details →

Figure 1 in Microbial diversity of ticks and a novel typhus group Rickettsia species (Rickettsiales bacterium Ac37b) in Inner Mongolia, China

Figure 1. Map of tick collection sites in Inner Mongolia, China.

opencc-zeroNov 2022View details →

Data for: Latent functional diversity may accelerate microbial community responses to temperature fluctuations

How complex microbial communities respond to climatic fluctuations remains an open question. Due to their relatively short generation times and high functional diversity, microbial populations harbor great potential to respond as a community through a combination of strain-level phenotypic plasticity, adaptation, and species sorting. However, the relative importance of these mechanisms remains unclear. We conducted a laboratory experiment to investigate the degree to which bacterial communities can respond to changes in environmental temperature through a combination of phenotypic plasticity and species sorting alone. We grew replicate soil communities from a single location at six temperatures between 4°C and 50°C. We found that phylogenetically- and functionally-distinct communities emerge at each of these temperatures, with K-strategist taxa favoured under cooler conditions, and r-strategist taxa under warmer conditions. We show that this dynamic emergence of distinct communities across a wide range of temperatures (in essence, community-level adaptation), is driven by the resuscitation of latent functional diversity: the parent community harbors multiple strains pre-adapted to different temperatures that are able to "switch on" at their preferred temperature without immigration or adaptation. Our findings suggest that microbial community function in nature is likely to respond rapidly to climatic temperature fluctuations through shifts in species composition by resuscitation of latent functional diversity.

opencc-zeroJan 2023View details →

Tree diversity effects on soil microbial biomass and respiration are context-dependent across forest diversity experiments

Aim Soil microorganisms are essential for the functioning of terrestrial ecosystems. Although soil microbial communities and functions may be linked to tree species composition and diversity, there has been no comprehensive study of how general these potential relationships are, or if they are context-dependent. Here, we examine tree diversity–soil microbial biomass and respiration relationships across environmental gradients using a global network of tree diversity experiments. Location Global Time Period 2013 Major Taxa Studied Soil microorganisms Methods Soil samples collected from eleven tree diversity experiments in four biomes were used to measure microbial respiration, biomass, and respiratory quotient using the substrate-induced respiration method. All samples were measured using the same analytical device, method, and procedure to reduce measurement bias. We used linear mixed-effects models and PCA to examine the effects of tree diversity (taxonomic and phylogenetic), environmental conditions, and interactions on soil microbial properties. Results Abiotic drivers, mainly soil water content, but also soil carbon and soil pH, significantly increased soil microbial biomass and respiration. Optimal soil water content reduced the importance of other abiotic drivers. Tree diversity alone had no effect on the soil microbial properties, but interactions with phylogenetic diversity indicated that diversity effects are context-dependent and stronger in drier soils. Similar results were found for soil carbon and soil pH. Main conclusions Our results point to the importance of abiotic variables and especially soil water content for maintaining high levels of soil microbial functions and modulating the effects of other environmental drivers. Planting tree species with diverse water-use strategies and structurally complex canopies and high leaf area may crucial for maintaining high soil microbial biomass and respiration. Since higher phylogenetic distance alleviated unfavorable soil water conditions, reforestation efforts accounting for traits improving soil water content or choosing more phylogenetically distant species may assist in increasing soil microbial functions.

opencc-zeroJun 2023View details →

Data from: Positive plant diversity effects on soil microbial drought resistance are linked to variation in labile carbon and microbial community structure

Biodiversity loss and drought are substantially altering both above-and belowground terrestrial ecosystem functioning, but mechanistic understanding of plant diversity effects on the drought resistance of soil microbial biomass remains limited. We designed a mesocosm experiment to examine drought resistance of soil microbial biomass along a plant species richness gradient (five plant species richness levels based on old-field communities). We calculated resistance of microbial biomass to drought and recorded key belowground properties which may influence microbial resistance to drought (i.e., microbial diversity, microbial community structure, soil carbon stocks and root biomass). Plant species richness had a positive effect on microbial resistance to drought. Variation in microbial resistance to drought was linked to properties of the fungal community in ambient soil (Shannon diversity, arbuscular mycorrhizal fungal richness and abundance) but not soil bacterial diversity. Moreover, microbial resistance to drought increased with increasing root biomass and dissolved organic carbon recorded under ambient conditions. These results highlight the importance of plant diversity for microbial biomass stability in our old-field study system with implications for biogeochemical cycling, and suggest that indirect effects of plant species richness on labile soil carbon and soil fungi may drive resistance of soil microbial biomass to drought.

opencc-zeroJun 2023View details →

Tree diversity effects on litter decomposition are mediated by litterfall and microbial processes

Forest ecosystems are critical for their carbon sequestration potential. Increasing tree diversity was shown to enhance both forest productivity and litter decomposition. Litter diversity increases litter decomposability by increasing the diversity of substrates offered to decomposers. However, the relative importance of litter decomposability and decomposer community in mediating tree diversity effects on decomposition remains unknown. Moreover, tree diversity modulation of litterfall spatial distribution, consequently, litter decomposition has rarely been tested. We studied tree diversity effects on leaf litter decomposition and its mediation by the amount of litterfall, litter species richness and decomposability, and soil microorganisms in a large-scale tree diversity experiment in subtropical China. Furthermore, we examined how litter functional identity and diversity affect leaf litter decomposability. Finally, we tested how leaf functional traits, tree biomass, and forest spatial structure drive the litterfall spatial distribution. We found evidence that tree species richness increased litter decomposition by increasing litter species richness and the amount of litterfall. We showed that soil microorganisms in this subtropical forest perform 84–87% of litter decomposition. Moreover, changes in the amount of litterfall and microbial decomposition explained 19–37% of the decomposition variance. Additionally, up to 20% of the microbial decomposition variance was explained by litter decomposability, while litter decomposability itself was determined by litter functional identity, diversity, and species richness. Tree species richness increased litter species richness and the amount of litterfall (+200% from monoculture to 8-species neighborhood). We further demonstrated that the amount of species-specific litterfall increased with increasing tree proximity and biomass and was modulated by leaf functional traits. These litterfall drivers increased the spatial heterogeneity of litter distribution, thus, litter decomposition. We highlighted multiple biomass- and diversity-mediated effects of tree diversity on ecosystem properties driving forest nutrient cycling. We conclude that considering spatial variability in biotic properties will improve our mechanistic understanding of ecosystem functioning.

publicJun 2022View details →

Soil microbial diversity and community composition during conversion from conventional to organic agriculture

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publicJun 2024View details →

Climate regulates the effect of land-use change on the diversity of soil microbial functional groups and soil multifunctionality

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