Metagenomic analysis of fungal assemblages at a regional scale in high-altitude temperate forest soils: alternative methods to determine diversity, composition and environmental drivers.

Background: Understanding the diversity and distribution of fungal communities at a regional scale is important since fungi play a crucial role in ecosystem functioning. Our study used environmental metagenomics to determine fungal communities in mountainous forest soils in the central highlands of Mexico.

Methods: We used four different bioinformatic workflows to profile fungal assemblages, .

The archaeal and bacterial community structure in composted cow manures is defined by the original populations: a shotgun metagenomic approach.

Introduction: Organic wastes are composted to increase their plant nutritional value, but little is known about how this might alter the bacterial and archaeal community structure and their genes.

Methods: Cow manure was collected from three local small-scale farmers and composted under controlled conditions, while the bacterial and archaeal communities were determined using shotgun metagenomics at the onset and after 74 days of composting.

Results: The bacterial, archaeal, methanogen, methanotrophs, methylotroph, and nitrifying community structures and their genes were affected by composting for 74 days, but the original composition of these communities determined the changes.

Structural and functional bacterial biodiversity in a copper, zinc and nickel amended bioreactor: shotgun metagenomic study.

Background: At lower concentrations copper (Cu), zinc (Zn) and nickel (Ni) are trace metals essential for some bacterial enzymes. At higher concentrations they might alter and inhibit microbial functioning in a bioreactor treating wastewater. We investigated the effect of incremental concentrations of Cu, Zn and Ni on the bacterial community structure and their metabolic functions by shotgun metagenomics.

Spatial and Temporal Shifts of Endophytic Bacteria in Conifer Seedlings of Abies religiosa (Kunth) Schltdl. & Cham.

Endophytes play an important role in plant development, survival, and establishment, but their temporal dynamics in young conifer plants are still largely unknown. In this study, the bacterial community was determined by metabarcoding of the 16S rRNA gene in the rhizoplane, roots, and aerial parts of 1- and 5-month-old seedlings of natural populations of Abies religiosa (Kunth) Schltdl. & Cham.

Maternal transmission of bacterial microbiota during embryonic development in a viviparous lizard.

We investigated the presence and diversity of bacteria in the embryos of the viviparous lizard and their amniotic environment. We compared this diversity to that found in the maternal intestine, mouth, and cloaca. We detected bacterial DNA in the embryos, albeit with a lower bacterial species diversity than found in maternal tissues.

Land-use change alters the bacterial community structure, but not forest management.

Deforestation has a large impact on soil fertility, especially on steep slopes, but by applying sustainable management practices, local communities in Oaxaca (Mexico) have tried to avoid the most negative effects on the forest ecosystems they manage. In this study, the characteristics and bacterial community structure were investigated from soil sampled in triplicate (n = 3) with different land use, i.e.

Nitrogen Fertilizer Application Alters the Root Endophyte Bacterial Microbiome in Maize Plants, but Not in the Stem or Rhizosphere Soil.

Plant-associated microorganisms that affect plant development, their composition, and their functionality are determined by the host, soil conditions, and agricultural practices. How agricultural practices affect the rhizosphere microbiome has been well studied, but less is known about how they might affect plant endophytes. In this study, the metagenomic DNA from the rhizosphere and endophyte communities of root and stem of maize plants was extracted and sequenced with the "diversity arrays technology sequencing," while the bacterial community and functionality (organized by subsystems from general to specific functions) were investigated in crops cultivated with or without tillage and with or without N fertilizer application.

Application of young maize plant residues alters the microbiome composition and its functioning in a soil under conservation agriculture: a metagenomics study.

To increase our knowledge on how application of organic material alters soil microbial populations and functionality, shotgun metagenomic sequencing was used to determine the microbial communities and their potential functionality in an arable soil amended with young maize plants (Zea mays L.) in a laboratory experiment after 3 days. The relative abundance of bacterial and viral groups was strongly affected by organic material application, whereas that of the archaeal, protist and fungal groups was less affected.

Bacteria in (vermi)composted organic wastes mostly survive when applied to an arable soil cultivated with wheat (Triticum sp. L.).

Composting and vermicomposting are an environmentally friendly way to reduce pathogens in organic wastes and generate a valuable product that provides nutrients for crops. However, how the bacterial community structure changes during these different processes and if the bacteria applied with the (vermi)composted products survive in an arable cultivated soil is still largely unknown. In this study, we monitored how the bacterial community structure changed during conditioning, composting with and without Eisenia fetida, and when the end-product was applied to arable soil cultivated with wheat Triticum sp.

Application of ammonium to a N limited arable soil enriches a succession of bacteria typically found in the rhizosphere.

Crop residue management and tillage are known to affect the soil bacterial community, but when and which bacterial groups are enriched by application of ammonium in soil under different agricultural practices from a semi-arid ecosystem is still poorly understood. Soil was sampled from a long-term agronomic experiment with conventional tilled beds and crop residue retention (CT treatment), permanent beds with crop residue burned (PBB treatment) or retained (PBC) left unfertilized or fertilized with 300 kg urea-N ha and cultivated with wheat (Triticum durum L.)/maize (Zea mays L.

Bacterial Communities in the Rhizosphere at Different Growth Stages of Maize Cultivated in Soil Under Conventional and Conservation Agricultural Practices.

Farmers in Mexico till soil intensively, remove crop residues for fodder and grow maize often in monoculture. Conservation agriculture (CA), including minimal tillage, crop residue retention and crop diversification, is proposed as a more sustainable alternative. In this study, we determined the effect of agricultural practices and the developing maize rhizosphere on soil bacterial communities.

Greenhouse gas emissions of biosolid and cow manure during composting and vermicomposting and when applied to soil cultivated with wheat (Triticum sp. L.).

Biosolids are a by-product of wastewater treatment, and their nutritional composition makes them ideal for fertilizing crops. However, pre-treatments, such as conditioning and/or (vermi)composting, are often required to stabilize the product and remove pathogens. Biosolids, cow manure, and a 50-50% mixture were conditioned for 21 days, composted or vermicomposted with Eisenia fetida (Savigny 1826) for 28 days, and applied to soil cultivated with wheat (Triticum sp.

Conversion of a High-Altitude Temperate Forest for Agriculture Reduced Alpha and Beta Diversity of the Soil Fungal Communities as Revealed by a Metabarcoding Analysis.

Land-use change is one of the most important drivers of change in biodiversity. Deforestation for grazing or agriculture has transformed large areas of temperate forest in the central highlands of Mexico, but its impact on soil fungal communities is still largely unknown. In this study, we determined how deforestation of a high-altitude temperate forest for cultivation of maize ( L.

Bacterial Communities in Alkaline Saline Soils Amended with Young Maize Plants or Its (Hemi)Cellulose Fraction.

We studied three soils of the former lake Texcoco with different electrolytic conductivity (1.9 dS m, 17.3 dS m, and 33.

Impact of a bacterial consortium on the soil bacterial community structure and maize (Zea mays L.) cultivation.

Microorganisms are often applied as biofertilizer to crops to stimulate plant growth, increase yields and reduce inorganic N application. The survival and proliferation of these allochthonous microorganisms in soil is a necessary requisite for them to promote plant growth. We applied a sterilized or unsterilized not commercialized bacterial consortium mixed with cow manure leachate used by a farmer as biofertilizer to maize (Zea mays L.

The root endophytic bacterial community of Ricinus communis L. resembles the seeds community more than the rhizosphere bacteria independent of soil water content.

Rhizosphere and root endophytic bacteria are crucial for plant development, but the question remains if their composition is similar and how environmental conditions, such as water content, affect their resemblance. Ricinus communis L., a highly drought resistant plant, was used to study how varying soil water content affected the bacterial community in uncultivated, non-rhizosphere and rhizosphere soil, and in its roots.

Dietary effects on gut microbiota of the mesquite lizard Sceloporus grammicus (Wiegmann, 1828) across different altitudes.

Background: High-altitude ecosystems are extreme environments that generate specific physiological, morphological, and behavioral adaptations in ectotherms. The shifts in gut microbiota of the ectothermic hosts as an adaptation to environmental changes are still largely unknown. We investigated the food ingested and the bacterial, fungal, and protistan communities in feces of the lizard Sceloporus grammicus inhabiting an altitudinal range using metabarcoding approaches.

Soil microbial diversity drops with land-use change in a high mountain temperate forest: a metagenomics survey.

Land-use change has been identified as the most severe threat to biodiversity. Soils are important biodiversity reservoirs, but to what extent conversion of high-altitude temperate forest to arable land affects taxonomic and functional soil biodiversity is still largely unknown. Shotgun metagenomics was used to determine the taxonomic and functional diversity of bacteria, archaea and DNA virus in terms of effective number of species in high-altitude temperate oak and pine-oak forest and arable soils from Mexico.

Land use is the main driver of soil organic carbon spatial distribution in a high mountain ecosystem.

Background: Terrestrial ecosystems play a significant role in carbon (C) storage. Human activities, such as urbanization, infrastructure, and land use change, can reduce significantly the C stored in the soil. The aim of this research was to measure the spatial variability of soil organic C (SOC) in the national park La Malinche (NPLM) in the central highlands of Mexico as an example of highland ecosystems and to determine the impact of land use change on the SOC stocks through deterministic and geostatistical geographic information system (GIS) based methods.

Microbial community dynamics during aerobic granulation in a sequencing batch reactor (SBR).

Microorganisms in aerobic granules formed in sequencing batch reactors (SBR) remove contaminants, such as xenobiotics or dyes, from wastewater. The granules, however, are not stable over time, decreasing the removal of the pollutant. A better understanding of the granule formation and the dynamics of the microorganisms involved will help to optimize the removal of contaminants from wastewater in a SBR.

TiO nanoparticles affect the bacterial community structure and (Savigny, 1826) in an arable soil.

The amount of nanoparticles (NP), such as TiO, has increased substantially in the environment. It is still largely unknown, however, how NP might interact with earthworms and organic material and how this might affect the bacterial community structure and their functionality. Therefore, an arable soil was amended with TiO NP at 0, 150 or 300 mg kg and subjected to different treatments.

Bacterial and archaeal spatial distribution and its environmental drivers in an extremely haloalkaline soil at the landscape scale.

Background: A great number of studies have shown that the distribution of microorganisms in the soil is not random, but that their abundance changes along environmental gradients (spatial patterns). The present study examined the spatial variability of the physicochemical characteristics of an extreme alkaline saline soil and how they controlled the archaeal and bacterial communities so as to determine the main spatial community drivers.

Methods: The archaeal and bacterial community structure, and soil characteristics were determined at 13 points along a 211 m transect in the former lake Texcoco.

The Bacterial Community Structure and Microbial Activity in a Traditional Organic Milpa Farming System Under Different Soil Moisture Conditions.

Agricultural practices affect the bacterial community structure, but how they determine the response of the bacterial community to drought, is still largely unknown. Conventional cultivated soil, i.e.

Correction to: Autolysis of Pichia pastoris induced by cold.

The original version of this article (Bartolo-Aguilar et al. 2017) was written and published including the first construction strategy of pLGC09, but not the final one. This error was pointed out by a reader and an analysis of sequences of parts of the plasmid corroborated this.