Biogels in Soils: Plant Mucilage as a Biofilm Matrix That Shapes the Rhizosphere Microbial Habitat

Mucilage is a gelatinous high-molecular-weight substance produced by almost all plants, serving numerous functions for plant and soil. To date, research has mainly focused on hydraulic and physical functions of mucilage in the rhizosphere. Studies on the relevance of mucilage as a microbial habitat are scarce. Extracellular polymeric substances (EPS) are similarly gelatinous high-molecular-weight substances produced by microorganisms. EPS support the establishment of microbial assemblages in soils, mainly through providing a moist environment, a protective barrier, and serving as carbon and nutrient sources. We propose that mucilage shares physical and chemical properties with EPS, functioning similarly as a biofilm matrix covering a large extent of the rhizosphere. Our analyses found no evidence of consistent differences in viscosity and surface tension between EPS and mucilage, these being important physical properties. With regard to chemical composition, polysaccharide, protein, neutral monosaccharide, and uronic acid composition also showed no consistent differences between these biogels. Our analyses and literature review suggest that all major functions known for EPS and required for biofilm formation are also provided by mucilage, offering a protected habitat optimized for nutrient mobilization. Mucilage enables high rhizo-microbial abundance and activity by functioning as carbon and nutrient source. We suggest that the role of mucilage as a biofilm matrix has been underestimated, and should be considered in conceptual models of the rhizosphere.

Ocean Aerobiology

Ocean aerobiology is defined here as the study of biological particles of marine origin, including living organisms, present in the atmosphere and their role in ecological, biogeochemical, and climate processes. Hundreds of trillions of microorganisms are exchanged between ocean and atmosphere daily. Within a few days, tropospheric transport potentially disperses microorganisms over continents and between oceans. There is a need to better identify and quantify marine aerobiota, characterize the time spans and distances of marine microorganisms’ atmospheric transport, and determine whether microorganisms acclimate to atmospheric conditions and remain viable, or even grow. Exploring the atmosphere as a microbial habitat is fundamental for understanding the consequences of dispersal and will expand our knowledge of biodiversity, biogeography, and ecosystem connectivity across different marine environments. Marine organic matter is chemically transformed in the atmosphere, including remineralization back to CO2. The magnitude of these transformations is insignificant in the context of the annual marine carbon cycle, but may be a significant sink for marine recalcitrant organic matter over long (∼104 years) timescales. In addition, organic matter in sea spray aerosol plays a significant role in the Earth’s radiative budget by scattering solar radiation, and indirectly by affecting cloud properties. Marine organic matter is generally a poor source of cloud condensation nuclei (CCN), but a significant source of ice nucleating particles (INPs), affecting the formation of mixed-phase and ice clouds. This review will show that marine biogenic aerosol plays an impactful, but poorly constrained, role in marine ecosystems, biogeochemical processes, and the Earth’s climate system. Further work is needed to characterize the connectivity and feedbacks between the atmosphere and ocean ecosystems in order to integrate this complexity into Earth System models, facilitating future climate and biogeochemical predictions.

The isolation and characterization of Taphrina betulina and other yeasts residing in the Betula pendula phylloplane.

The phylloplane is an important microbial habitat and a reservoir of organisms that affect plant health, both positively and negatively. Taphrina betulina is the causative agent of birch witches′ broom disease. Taphrina are dimorphic, invading theirs hosts in a filamentous form and residing in the host phyllosphere in their non-infectious yeast form. As such, they are widely accepted to be found a resident yeasts on their hosts, even on healthy tissues; however, there is little experimental data to support this. With the aim of exploring the local infection ecology of T. betulina, we have isolated yeasts from the phylloplane of birch, using three classes of samples; from infected symptom bearing leaves inside brooms, healthy leaves from branches away from brooms on broom bearing trees, and symptom-free leaves from symptom-free trees. Isolations yielded 224 yeast strains, representing 11 taxa, including T. betulina, which was the most common isolate and was found in all sample classes, including asymptomatic leaves. Genotyping with two genetic markers revealed genetic diversity among these T. betulina isolates, with seven distinct genotype differentiated by the markers used. Of the 57 T. betulina strains, 22 representative strains were selected for further studies and preliminarily characterized, revealing differences in size and the ability to produced compounds with activity to activate the signalling pathway for the plant hormone auxin.

Bacterial Extracellular Polymers: A Review

Prokaryotic microbial cells especially bacteria are highly emphases for their exopolysaccharides (EPS) production. EPS are the higher molecular weight natural extracellular compounds observe at the surface of the bacterial cells. Nowadays bacterial EPS represent rapidly emerging as new and industrially important biomaterials because it having tremendous physical and chemical properties with novel functionality. Due to its industrial demand as well as research studies the different extraction processes have been discovered to remove the EPS from the microbial biofilm. The novelties of EPS are also based on the microbial habitat conditions such as higher temperature, lower temperature, acidic, alkaliphilic, saline, etc. Based on its chemical structure they can be homopolysaccharide or heteropolysaccharide. EPSs have a wide range of applications in various industries such as food, textile, pharmaceutical, heavy metal recovery, agriculture, etc. So, this review focus on the understanding of the structure, different extraction processes, biosynthesis and genetic engineering of EPS as well as their desirable biotechnological applications.

Metagenomic Outlooks of Microbial Dynamics Influenced by Organic Manure in Tea Garden Soils of North Bengal, India

Soil being the most heterogeneous and complex microbial habitat on earth exceeds the quantity of inhabiting microbial communities than other environments. Next-generation sequencing (NGS) based metagenomics provides us directs access to the uncultivated genomes. In this study, we targeted two very popular tea gardens of Darjeeling hills- Makaibari (Mak) and Castleton (Cas). The main difference between them is the type of manure they use. Mak is solely an organic tea garden using all organic manure and fertilizers whereas Cas uses inorganic pesticides and fertilizers. The main aim was to compare the effect of organic manure over chemical fertilizers on the soil microbiome as well as the health of tea garden workers. We have performed the 16s metagenomics analysis based on V3-V4 region. Downstream bioinformatics analysis including Reverse Ecology was performed. We found that the overall microbial diversity is higher in Mak rather than Cas. Moreover, the use of organic manure has reduced the population of pathogenic bacteria in Mak soil when compared to Cas soil thus having an indirect effect on the heath of the tea garden workers. From the observations made through the metagenomics analysis of Mak and Cas soil samples we may propose that the application of organic manure supports the population of good bacteria in the soil which eventually can have a better impact on the tea garden workers.

Development of A Manometric Monitoring Method for Early Detection of Air Microbiological Contamination in the Bloodstream

Atmospheric air is a microbial habitat of pathogenic bioaerosols that may pose serious risks to humans. A commonly laboratory-based approach for the diagnosis of such infections in the bloodstream is the blood culture analysis. Its clinical relevance is attributed to the fact that these infections are characterized by high rates of morbidity and mortality, requiring the need for efficient methods for rapid diagnosis. For this reason, our study aimed to develop a method of manometric monitoring for the rapid detection of viable microorganisms in blood culture vials. A methodology was developed to detect pressure variation in intra-vials through a manometric instrument that was coupled to vials of blood culture containing culture broth that allowed microbial growth. This device allowed the early detection of microbial activity based on the production or use of intra-flask gases as a result of microbial metabolic activity. The analyzed variables were the pressure as a function of time, microbial species, and culture medium. The highest pressure found in the flasks without microorganisms was 40 mmHg between 2 and 6 h, and the lowest pressure was −42 mmHg between 21 and 24 h. The variation of the internal pressure in blood culture flasks according to different groups of microorganisms as a function of time demonstrated that the fermentative gram-negative bacilli and gram-positive cocci exhibited a significant increase in relation to their respective control groups (p < 0.001). The non-fermenting gram-negative bacilli showed expected results in relation to the pressure variation in which the production of negative pressures was noticed during the period of analysis, with a significant difference with respect to their control groups (p < 0.001). The developed methodology for the early detection of microorganisms responsible for bloodstream infection was demonstrated to be effective.

A metagenomic view of novel microbial and metabolic diversity found within the deep terrestrial biosphere

The deep terrestrial subsurface is a large and diverse microbial habitat and a vast repository of biomass. However, in relation to its size and physical heterogeneity we have limited understanding of taxonomic and metabolic diversity in this realm. Here we present a detailed metagenomic analysis of samples from the Deep Mine Microbial Observatory (DeMMO) spanning depths from the surface to 1.5 km deep in the crust. From these eight geochemically and spatially distinct fluid samples we reconstructed ~600 metagenome assembled genomes (MAGs), representing 50 distinct phyla and including 18 candidate phyla. These novel clades include many members of the Patescibacteria superphylum and two new MAGs from candidate phylum OLB16, a phylum originally identified in DeMMO fluids and for which only one other MAG is currently available. We find that microbes spanning this expansive phylogenetic diversity and physical space are often capable of numerous dissimilatory energy metabolisms and are poised to take advantage of nutrients as they become available in relatively isolated fracture fluids. This metagenomic dataset is contextualized within a four-year geochemical and 16S rRNA time series, adding another invaluable piece to our knowledge of deep subsurface microbial ecology.

The Habitat Filters of Microbiota-Nourishing Immunity

An imbalance in the microbiota may contribute to many human illnesses, which has prompted efforts to rebalance it by targeting the microbes themselves. However, by supplying the habitat, the host wields a prominent influence over microbial growth at body surfaces, raising the possibility that rebalancing the microbiota by targeting our immune system would be a viable alternative. Host control mechanisms that sculpt the microbial habitat form a functional unit with the microbiota, termed microbiota-nourishing immunity, that confers colonization resistance against pathogens. The host components of microbiota-nourishing immunity can be viewed as habitat filters that select for microbial traits licensing growth and survival in host habitat patches. Here we review current knowledge of how host-derived habitat filters shape the size, species composition, and spatial heterogeneity of the microbiota and discuss whether these host control mechanisms could be harnessed for developing approaches to rebalance microbial communities during dysbiosis.

Effects of Biochar on Properties of Tropical Sandy Soils Under Organic Agriculture

This study evaluated the influences of biochar made from local agricultural wastes on sandy soils in farmer fields where biochar has been used as a soil amendment for more than three years. The major objective of this study was to gain insight into the effects of long-term biochar application on properties of sandy soil. Unamended soil properties were compared to biochar-amended soils properties using the paired samples t-test (p &lt; 0.05). The statistical results of the study indicated that cation exchange capacity, exchangeable potassium, available phosphorus, field capacity, plant available water, water-stable aggregate size fractions (&gt; 1 and &lt; 0.25 mm), median aggregate size and aggregate stability were significantly different at p &lt; 0.05. Clearly, biochar present for 3 or more years can improve soil physicochemical properties. We conclude that sandy soil properties, especially soil physical properties, are very strongly affected by biochar application combined with conservative soil management. Biochars affect both physical and biological mechanisms of soil aggregate formation because the biochar particle sizes influence the arrangement of clay on biochar and biochar grains provide a favorable microbial habitat and food source for fungi creating microorganism-biochar-soil associations which enhance water-stable aggregates and water holding capacity.

Tracking the Deep Biosphere through Time

The oceanic and continental lithosphere constitutes Earth’s largest microbial habitat, yet it is scarcely investigated and not well understood. The physical and chemical properties here are distinctly different from the overlaying soils and the hydrosphere, which greatly impact the microbial communities and associated geobiological and geochemical processes. Fluid–rock interactions are key processes for microbial colonization and persistence in a nutrient-poor and extreme environment. Investigations during recent years have spotted microbial processes, stable isotope variations, and species that are unique to the subsurface crust. Recent advances in geochronology have enabled the direct dating of minerals formed in response to microbial activity, which in turn have led to an increased understanding of the evolution of the deep biosphere in (deep) time. Similarly, the preservation of isotopic signatures, as well as organic compounds within fossilized micro-colonies or related mineral assemblages in voids, cements, and fractures/veins in the upper crust, provides an archive that can be tapped for knowledge about ancient microbial activity, including both prokaryotic and eukaryotic life. This knowledge sheds light on how lifeforms have evolved in the energy-poor subsurface, but also contributes to the understanding of the boundaries of life on Earth, of early life when the surface was not habitable, and of the preservation of signatures of ancient life, which may have astrobiological implications. The Special Issue “Tracking the Deep Biosphere through Time” presents a collection of scientific contributions that provide a sample of forefront research in this field. The contributions involve a range of case studies of deep ancient life in continental and oceanic settings, of microbial diversity in sub-seafloor environments, of isolation of calcifying bacteria as well as reviews of clay mineralization of fungal biofilms and of the carbon isotope records of the deep biosphere.