scholarly journals Holocene life and microbiome profiling in ancient tropical Lake Chalco, Mexico

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Bárbara Moguel ◽  
Liseth Pérez ◽  
Luis D. Alcaraz ◽  
Jazmín Blaz ◽  
Margarita Caballero ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Fungal Pathogens ◽  
Environmental Changes ◽  
Human Impacts ◽  
Protein Family ◽  
Near Surface ◽  
Tropical Regions ◽  
Carbon Cycles ◽  
Microbiome Profiling ◽  
Early Human

AbstractMetagenomic and traditional paleolimnological approaches are suitable to infer past biological and environmental changes, however, they are often applied independently, especially in tropical regions. We combined both approaches to investigate Holocene Prokaryote and Eukaryote diversity and microbial metabolic pathways in ancient Lake Chalco, Mexico. Here, we report on diversity among a large number of lineages (36,722 OTUs) and functional diversity (27,636,243 non-clustered predicted proteins, and 6,144 annotated protein-family genes). The most abundant domain is Bacteria (81%), followed by Archaea (15%) and Eukarya (3%). We also determined the diversity of protein families and their relationship to metabolic pathways. The early Holocene (> 11,000 cal years BP) lake was characterized by cool, freshwater conditions, which later became warmer and hyposaline (11,000–6,000 cal years BP). We found high abundances of cyanobacteria, and fungi groups associated with mature forests in these sediments. Bacteria and Archaea include mainly anaerobes and extremophiles that are involved in the sulfur, nitrogen, and carbon cycles. We found evidence for early human impacts, including landscape modifications and lake eutrophication, which began ~ 6,000 cal years BP. Subsaline, temperate conditions were inferred for the past 5,000 years. Finally, we found nitrogen-fixing bacteria and protein-family genes that are linked to contaminated environments, as well as several fungal pathogens of crops in near-surface sediments.

scholarly journals General Unified Microbiome Profiling Pipeline (GUMPP) for Large Scale, Streamlined and Reproducible Analysis of Bacterial 16S rRNA Data to Predicted Microbial Metagenomes, Enzymatic Reactions and Metabolic Pathways

Metabolites ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 336
Author(s):  
Boštjan Murovec ◽  
Leon Deutsch ◽  
Blaž Stres
Keyword(s):  
16S Rrna ◽  
Metabolic Pathways ◽  
Large Scale ◽  
Enzymatic Reactions ◽  
Operational Taxonomic Units ◽  
Biochemical Pathways ◽  
Meaningful Information ◽  
Novel Biomarkers ◽  
Reproducible Analysis ◽  
Microbiome Profiling

General Unified Microbiome Profiling Pipeline (GUMPP) was developed for large scale, streamlined and reproducible analysis of bacterial 16S rRNA data and prediction of microbial metagenomes, enzymatic reactions and metabolic pathways from amplicon data. GUMPP workflow introduces reproducible data analyses at each of the three levels of resolution (genus; operational taxonomic units (OTUs); amplicon sequence variants (ASVs)). The ability to support reproducible analyses enables production of datasets that ultimately identify the biochemical pathways characteristic of disease pathology. These datasets coupled to biostatistics and mathematical approaches of machine learning can play a significant role in extraction of truly significant and meaningful information from a wide set of 16S rRNA datasets. The adoption of GUMPP in the gut-microbiota related research enables focusing on the generation of novel biomarkers that can lead to the development of mechanistic hypotheses applicable to the development of novel therapies in personalized medicine.

scholarly journals New kid on the block: Research of alpine-lake macroinvertebrates in the Tatra Mountains enhanced by DNA barcoding and metabarcoding

2021 ◽  
Vol 4 ◽  
Author(s):  
Ondrej Vargovčík ◽  
Zuzana Čiamporová-Zaťovičová ◽  
Fedor Čiampor Jr
Keyword(s):  
Large Scale ◽  
Environmental Changes ◽  
Human Impacts ◽  
Sampling Error ◽  
Alpine Lakes ◽  
Alpine Lake ◽  
Tatra Mountains ◽  
Aquatic Communities ◽  
Wide Range ◽  
The Tatra Mountains

State of ecosystems and biodiversity protection are becoming the key interests for modern society due to climate change and negative human impacts (Leese 2018). Environmental changes in freshwaters are indicated also by benthic communities, especially in sensitive ecosystems like alpine lakes (Fjellheim 2009). Moreover, remoteness and isolation of alpine lakes make them a source of biodiversity, which is worth conserving (Hamerlík 2014). A promising tool for efficient large-scale monitoring of aquatic communities is DNA metabarcoding (Leese 2018). In this study, we applied metabarcoding to analyse macrozoobenthos of 12 lakes in the Tatra Mountains, using benthic bulk samples and eDNA filtered from water (Fig. 1). In compliance with recent publications, eDNA amplified with BF3/BR2 primers resulted in high percentage of non-invertebrate reads (Leese 2021). Based on in silico tests with the obtained sequences, we confirm that the recently developed EPTDr2n primer enables minimizing non-target amplification even with eDNA filtered from alpine-lake water (Elbrecht and Leese 2017). This ability is facilitated by 3’ end of the primer and we observed the two important mismatches in non-target sequences from our study (Leese 2021). Thus, our future analyses of eDNA (and bulk-sample fixative) will benefit from the new primer. Concerning bulk samples, a wide range of invertebrate taxa was assigned to the OTUs and they showed good congruence with previous studies using morphological determination (e.g. Krno 2006). Certain differences with (and among) the previous records per lake were observed, which could suggest ecological changes, but at the moment the influence of sampling error cannot be excluded. In eDNA, several taxa were congruent with the previous records, but their amount and read abundance was considerably lower due to non-target amplification. Apart from that, filling gaps in barcoding databases remains one of our priorities, as identification to species or genus level was not yet possible for some invertebrate OTUs. In addition, we subjected the NGS data to denoising and abundance-filtering in order to explore haplotype-level diversity (Andújar 2021). Although more comprehensive conclusions will be possible only after obtaining data from more lakes and years, already the two metabarcoding experiments presented here enabled us to efficiently detect within-species genetic diversity and identify a large variety of taxa, including groups that would otherwise be omitted or very challenging to identify. This underlines the potential of DNA methods to provide valuable ecological and biodiversity data across the tree of life for modern biomonitoring. This study was realized with support from VEGA 2/0030/17 and VEGA 2/0084/21.

Future Environments of South America

2007 ◽  
Author(s):  
Thomas T. Veblen ◽  
Kenneth R. Young
Keyword(s):  
South America ◽  
Environmental Change ◽  
Environmental Changes ◽  
Human Impacts ◽  
Southern Oscillation ◽  
Physical Geography ◽  
Tierra Del Fuego ◽  
South American ◽  
Policy Options ◽  
Natural Processes

An important goal of this book has been to provide a comprehensive understanding of the physical geography and landscape origins of South America as important background to assessing the probabilities and consequences of future environmental changes. Such background is essential to informed discussions of environmental management and the development of policy options designed to prepare local, national, and international societies for future changes. A unifying theme of this book has been the elucidation of how natural processes and human activities have interacted in the distant and recent past to create the modern landscapes of the continent. This retrospective appreciation of how the current landscapes have been shaped by nature and humans will guide our discussion of possible future trajectories of South American environments. There is abundant evidence from all regions of South America, from Tierra del Fuego to the Isthmus of Panama, that environmental change, not stasis, has been the norm. Given that fact, the history, timing, and recurrence intervals of this dynamism are all crucial pieces of information. The antiquity and widespread distribution of changes associated with the indigenous population are now well established. Rates and intensities of changes related to indigenous activities varied widely, but even in regions formerly believed to have experienced little or no pre-European impacts we now recognize the effects of early humans on features such as soils and vegetation. Colonization by Europeans mainly during the sixteenth century modified or in some cases replaced indigenous land-use practices and initiated changes that have continued to the present. Complementing these broad historical treatments of human impacts, other chapters have examined in detail the environmental impacts of agriculture (chapter 18) and urbanism (chapter 20), and the disruptions associated with El Niño–Southern Oscillation events. The goal of this final synthesis is to identify the major drivers of change and to discuss briefly their likely impacts on South American environments and resources in the near and medium-term future. Our intent is not to make or defend predictions, but rather to identify broad causes and specific drivers of environmental change to inform discussions of policy options for mitigating undesirable changes and to facilitate potential societal adaptations to them.

scholarly journals Enhancing Radiocarbon Chronologies of Colonization: Chronometric Hygiene Revisited

Radiocarbon ◽  
2019 ◽  
Vol 61 (2) ◽  
pp. 629-647 ◽  
Author(s):  
Magdalena M E Schmid ◽  
Rachel Wood ◽  
Anthony J Newton ◽  
Orri Vésteinsson ◽  
Andrew J Dugmore
Keyword(s):  
Climate Change ◽  
Environmental Changes ◽  
Human Impacts ◽  
Ice Core ◽  
Bayesian Models ◽  
Island Colonization ◽  
Sound Theory ◽  
People First

ABSTRACTAccurately dating when people first colonized new areas is vital for understanding the pace of past cultural and environmental changes, including questions of mobility, human impacts and human responses to climate change. Establishing effective chronologies of these events requires the synthesis of multiple radiocarbon (14C) dates. Various “chronometric hygiene” protocols have been used to refine 14C dating of island colonization, but they can discard up to 95% of available 14C dates leaving very small datasets for further analysis. Despite their foundation in sound theory, without independent tests we cannot know if these protocols are apt, too strict or too lax. In Iceland, an ice core-dated tephrochronology of the archaeology of first settlement enables us to evaluate the accuracy of 14C chronologies. This approach demonstrated that the inclusion of a wider range of 14C samples in Bayesian models improves the precision, but does not affect the model outcome. Therefore, based on our assessments, we advocate a new protocol that works with a much wider range of samples and where outlying 14C dates are systematically disqualified using Bayesian Outlier Models. We show that this approach can produce robust termini ante quos for colonization events and may be usefully applied elsewhere.

scholarly journals Investigation of the EIL/EIN3 Transcription Factor Gene Family Members and Their Expression Levels in the Early Stage of Cotton Fiber Development

Plants ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 128 ◽  
Author(s):  
Haron Salih ◽  
Shoupu He ◽  
Hongge Li ◽  
Zhen Peng ◽  
Xiongming Du
Keyword(s):  
Transcription Factor ◽  
Gene Family ◽  
Cotton Fiber ◽  
Metabolic Pathways ◽  
Higher Plants ◽  
Fiber Development ◽  
Protein Family ◽  
Sequencing Analysis ◽  
Cotton Fiber Development ◽  
Cotton Species

The ethylene-insensitive3-like/ethylene-insensitive3 (EIL/EIN3) protein family can serve as a crucial factor for plant growth and development under diverse environmental conditions. EIL/EIN3 protein is a form of a localized nuclear protein with DNA-binding activity that potentially contributes to the intricate network of primary and secondary metabolic pathways of plants. In light of recent research advances, next-generation sequencing (NGS) and novel bioinformatics tools have provided significant breakthroughs in the study of the EIL/EIN3 protein family in cotton. In turn, this paved the way to identifying and characterizing the EIL/EIN3 protein family. Hence, the high-throughput, rapid, and cost-effective meta sequence analyses have led to a remarkable understanding of protein families in addition to the discovery of novel genes, enzymes, metabolites, and other biomolecules of the higher plants. Therefore, this work highlights the recent advance in the genomic-sequencing analysis of higher plants, which has provided a plethora of function profiles of the EIL/EIN3 protein family. The regulatory role and crosstalk of different metabolic pathways, which are apparently affected by these transcription factor proteins in one way or another, are also discussed. The ethylene hormone plays an important role in the regulation of reactive oxygen species in plants under various environmental stress circumstances. EIL/EIN3 proteins are the key ethylene-signaling regulators and play important roles in promoting cotton fiber developmental stages. However, the function of EIL/EIN3 during initiation and early elongation stages of cotton fiber development has not yet been fully understood. The results provided valuable information on cotton EIL/EIN3 proteins, as well as a new vision into the evolutionary relationships of this gene family in cotton species.

Long-term herbivore population dynamics in the northeastern Qinghai-Tibetan Plateau and its implications for early human impacts

2020 ◽  
Vol 275 ◽  
pp. 104171 ◽  
Author(s):  
Xiaozhong Huang ◽  
Jun Zhang ◽  
Michael Storozum ◽  
Sisi Liu ◽  
Jacquelyn L. Gill ◽  
...  
Keyword(s):  
Population Dynamics ◽  
Tibetan Plateau ◽  
Human Impacts ◽  
Early Human

scholarly journals Chromatin-Mediated Regulation of Genome Plasticity in Human Fungal Pathogens

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 855 ◽  
Author(s):  
Buscaino
Keyword(s):  
Candida Albicans ◽  
Aspergillus Fumigatus ◽  
Cryptococcus Neoformans ◽  
Fungal Pathogens ◽  
Environmental Changes ◽  
Structure And Function ◽  
Model Systems ◽  
Genome Plasticity ◽  
And Function ◽  
Heterochromatin Structure

Human fungal pathogens, such as Candida albicans, Aspergillus fumigatus and Cryptococcus neoformans, are a public health problem, causing millions of infections and killing almost half a million people annually. The ability of these pathogens to colonise almost every organ in the human body and cause life-threating infections relies on their capacity to adapt and thrive in diverse hostile host-niche environments. Stress-induced genome instability is a key adaptive strategy used by human fungal pathogens as it increases genetic diversity, thereby allowing selection of genotype(s) better adapted to a new environment. Heterochromatin represses gene expression and deleterious recombination and could play a key role in modulating genome stability in response to environmental changes. However, very little is known about heterochromatin structure and function in human fungal pathogens. In this review, I use our knowledge of heterochromatin structure and function in fungal model systems as a road map to review the role of heterochromatin in regulating genome plasticity in the most common human fungal pathogens: Candida albicans, Aspergillus fumigatus and Cryptococcus neoformans.

scholarly journals Temporal Gene Expression Profiling of the Wheat Leaf Rust Pathosystem Using cDNA Microarray Reveals Differences in Compatible and Incompatible Defence Pathways

2007 ◽  
Vol 2007 ◽  
pp. 1-13 ◽  
Author(s):  
Bourlaye Fofana ◽  
Travis W. Banks ◽  
Brent McCallum ◽  
Stephen E. Strelkov ◽  
Sylvie Cloutier
Keyword(s):  
Leaf Rust ◽  
Metabolic Pathways ◽  
Fungal Pathogens ◽  
Puccinia Triticina ◽  
Phenylpropanoid Pathway ◽  
Altered Expression ◽  
Temporal Gene Expression ◽  
Wheat Leaf ◽  
Mock Treatment ◽  
Host Genes

In this study, we detail the construction of a custom cDNA spotted microarray containing 7728 wheat ESTs and the use of the array to identify host genes that are differentially expressed upon challenges with leaf rust fungal pathogens. Wheat cultivar RL6003 (Thatcher Lr1) was inoculated with Puccinia triticina virulence phenotypes BBB (incompatible) or TJB (7-2) (compatible) and sampled at four different time points (3, 6, 12, and 24 hours) after inoculation. Transcript expression levels relative to a mock treatment were measured. One hundred ninety two genes were found to have significantly altered expression between the compatible and incompatible reactions. Among those were genes involved in photosynthesis, the production of reactive oxygen species, ubiquitination, signal transduction, as well as in the shikimate/phenylpropanoid pathway. These data indicate that various metabolic pathways are affected, some of which might be used by RL6003 to mount a coordinated defense against an incompatible fungal pathogen.

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