Biodiversity Of Microorganisms Research Articles

Biodiversity of Microorganisms in the Aquatic Environment as a Source for Combating Phytopathogenic Fungi

Biodiversity of Microorganisms in the Aquatic Environment as a Source for Combating Phytopathogenic Fungi

Study of the dynamics of the microbial communities in the wedge clam Donax trunculus (Linnaeus, 1758) from the Bulgarian aquatory of the Black Sea

In the present work, we investigated the dynamics of the microbial communities in the wedge clam Donax trunculus (Linnaeus, 1758) from the Bulgarian coastal waters of the Black Sea. The samples were collected in the period of January 2020 until December 2022 from Arkutino, Ahtopol, Obzor and Tsarevo. The BIOLOG system was used for microbiological determination. In our investigation were isolated the following microorganisms: Enterococcus cancerogenus, Enterococcus hirae, Escherichia vulneris, Citrobacter farmeri, Acinetobacter gyllenbergii, Enterococcus hirae, Escherichia vulneris, Enterobacter cloacae, Escherichia hermannii, Pseudomonas mendocina, Pseudomonas fulva, Pseudomonas alcaligenes, Pseudomonas putida, Acinetobacter johnsonii, Acinetobacter gyllenbergii, Enterococcus hirae, Escherichia vulneris, Enterococcus gallinarum, Citrobacter sedakii, Pseudomonas putida, Streptococcus lugdunensis, Enterococcus casseliflavus, Vibrio cincinnatiensis, Vibrio alginolyticus, Vibrio parahaemolyticus, Enterococcus hirae, Streptococcus aureus, Staphylococcus lugdunensis and Enterococcus casseliflavus. During the winter period, we detected the presence of Pseudomonas sp. – P. alcaligenes, P. putida, and A. gyllenbergii. In the autumn months we isolated C. sedakii, C. farmeri, A. gyllenbergii, A. johnsonii, P. fulva and E. casseliflavus. In the spring, E. cancerogenus, E. hirae and Pseudomonas mendocina were found. During the summer, the highest biodiversity of microorganisms - E. hirae, E. vulneris, E. cloacae, E. gallinarum, P. putida, V. cincinnatiensis, V. alginolyticus, V. parahaemolyticus, S. aureus, E. hermannii and S. lugdunensis were registered. Although our three-year research showed that some species are permanent and others are transient, we tend to accept the conclusion that there is only a transient microbiota in mussels and it changes depending on environmental conditions or is a result of pollution of the Black Sea.

Revealing the Adverse Impact of Additive Carbon Material on Microorganisms and Its Implications for Biogas Yields: A Critical Review

Biochar could be a brilliant additive supporting the anaerobic fermentation process. However, it should be taken into account that in some cases it could also be harmful to microorganisms responsible for biogas production. The negative impact of carbon materials could be a result of an overdose of biochar, high biochar pH, increased arsenic mobility in the methane fermentation solution caused by the carbon material, and low porosity of some carbon materials for microorganisms. Moreover, when biochar is affected by an anaerobic digest solution, it could reduce the biodiversity of microorganisms. The purpose of the article is not to reject the idea of biochar additives to increase the efficiency of biogas production, but to draw attention to the properties and ways of adding these materials that could reduce biogas production. These findings have practical relevance for organizations seeking to implement such systems in industrial or local-scale biogas plants and provide valuable insights for future research. Needless to say, this study will also support the implementation of biogas technologies and waste management in implementing the idea of a circular economy, further emphasizing the significance of the research.

Properties of the extracellular alkaline inulinase produced by haloalkaliphilic phototrophic bacteria Ectothiorodospirea mobilis.

The studies have revealed alkaline exoinulinase produced by haloalkaliphilic phototrophic bacteria Ectothiorhodospirea mobilis Al-2 for the first time. A new method for the isolation of a homogeneous exoinulinase from the culture broth was developed and the properties of this enzyme have been investigated. It was shown that specified exoinulinase in contrast to the studied exoinulinases produced by microorganisms exhibits catalytic activity at the wide range of pH (7.0-10) and a temperature (20-60°C) with a maximum of the inulolitic activity at pH 9.0 and 50°C. The studied exoinulinase possessing also invertase activity (I/S1.4) is a monomeric protein with molecular mass 57Kda, as well as Km and Vmax for inulin 3.8mM/ml and 10µmol/ml/min-1, respectively. The studies of the influence of different metal ions on enzyme activity have shown that Mn+2, Cu+2,Co+2,Mg+2, NaCl 5-7% promote relatively higher catalytic activity while Zn+2, Cu+2and Fe+2partially suppress the enzyme activity and Hg2+completely inactivates the enzyme.The formation of only fructose and glucose at the enzymatic hydrolysis of inulin confirms that the studied exoinulinase belongs to the exo-type of enzymes. The obtained results supplement our fundamental knowledge in biochemistry-enzymology, as well as the biodiversity of microorganisms expressing exoinulinase. The studied exoinulinase exhibits activity at salinity of the medium and can potentially be used in the biotechnology of inulin bioconversion into bioproducts under alkaline conditions.

Soil sampling methods for microbial study in montane regions

Soil microorganism studies are crucial in ecological and biological research. However, the lack of standardized analytical methods for sampling makes it challenging to compare studies and obtain consistent results. Therefore, it is essential to establish standardized sampling methods in the field. Our study used a stratification method to collect 120 soil samples from various altitudinal ranges on Cangshan Mountain in China, with an altitude of 4122 m, and incredible microorganism biodiversity. This site provides an ideal landscape for studying elevation patterns in microorganisms. We conducted analyses on the variations of depth and stratification used in the sampling process, as these factors have been found to impact microbial diversity, elevation patterns, and community assembly mechanisms. We found that increasing the sampling depth provided more valuable research results by revealing elevation patterns of soil microorganisms. We therefore recommend sampling to a depth of 35 cm with stratification to determine the overall soil microbial diversity. A depth of 25 cm is suitable for studying elevation patterns with stratification. For investigating community assembly mechanisms without stratification, a depth of 15 cm is recommended. When exploring a specific taxon, the sampling depth can be adjusted accordingly. For studying the elevation pattern of archaea, a depth of 20 cm is appropriate. In the case of fungi, a depth of 40 cm is recommended, while a depth of 20 cm is suitable for studying elevation patterns. This study emphasizes the importance of standardization in sampling methods, particularly along the soil profiles, when studying soil microbiomes in montane areas. These recommendations should be adopted in future research to achieve more consistent and reliable results in the field.

A dataset of micro biodiversity in benthic sediment at a global scale

Microorganisms, occupying the largest biomass in deep sea, play essential roles in deep-sea ecosystem. It is believed that the microbes in deep-sea sediments are more representative of deep-sea microbial communities, the microbial composition of which is seldom affected by ocean currents. However, the community of benthic microbes on a global scale has not been adequately explored. Herein, we build a comprehensive global dataset determined by 16S rRNA gene sequencing to characterize the biodiversity of microorganisms in benthic sediment. The dataset comprised 212 records from 106 sites, included sequencing of bacteria and archaea for each site and yielded 4,766,502 and 1,562,989 reads, respectively. Through annotation, a total of 110,073 and 15,795 OTUs of bacteria and archaea were obtained, and 61 bacterial phyla and 15 archaeal phyla were identified, of which the dominant phyla were Proteobacteria and Thaumarchaeota in deep-sea sediment. Therefore, our findings provided a biodiversity data of microbial communities in deep-sea sediment at global-scale and laid a foundation to further reveal the structures of microorganism communities in deep sea.

Diversity of cellulolytic fungi in different land use systems in the Amazon

Quantitative assessments of the population density of the microbial community in soils are important to establish ecological relationships that occur in the soil and to identify factors that influence the management of agroecosystems. Therefore, the objective was to quantify the cellulolytic fungi present in the soils of three use and management systems in the Amazon. The studied areas consisted of intercropped cultivation with gliricidia, orange and banana; area with orange and forest essence and native forest area. In each area, soil samples were collected at depths of 0-10 and 10-20 cm, placed in sterile plastic bags, duly identified, and stored in a thermal box and later in a cold chamber (4 ºC). The quantification of cellulolytic organisms was obtained by suspending the soil, using a specific culture medium. The cultures were incubated in a B.O.D oven at 28°C for 37 days. The estimate of the number of viable cells was made using the most likely number (MPN). The results show that the soil with the gliricidia, orange and banana intercropping has a higher population of cellulolytic microorganisms, this group is strongly influenced by the local vegetation cover, thus proving to be an alternative for intercropping systems with agricultural crops, providing a greater biodiversity of microorganisms in the soil, in addition to helping to provide nutrients for the species.

Use of Microbial Consortia in Bioremediation of Metalloid Polluted Environments.

Metalloids are released into the environment due to the erosion of the rocks or anthropogenic activities, causing problems for human health in different world regions. Meanwhile, microorganisms with different mechanisms to tolerate and detoxify metalloid contaminants have an essential role in reducing risks. In this review, we first define metalloids and bioremediation methods and examine the ecology and biodiversity of microorganisms in areas contaminated with these metalloids. Then we studied the genes and proteins involved in the tolerance, transport, uptake, and reduction of these metalloids. Most of these studies focused on a single metalloid and co-contamination of multiple pollutants were poorly discussed in the literature. Furthermore, microbial communication within consortia was rarely explored. Finally, we summarized the microbial relationships between microorganisms in consortia and biofilms to remove one or more contaminants. Therefore, this review article contains valuable information about microbial consortia and their mechanisms in the bioremediation of metalloids.

A first insight into the Polish Bochnia Salt Mine metagenome

The Bochnia Salt Mine is one of the oldest mines in Europe. It was established in the thirteenth century, and actively operated until 1990. The mine has been placed on the UNESCO World Heritage List. Previous research describing Polish salt mines has been focused on bioaerosol characteristics and the identification of microorganisms potentially important for human health. The use of Polish salt mines as inhalation chambers for patients of health resorts has also been investigated. Nevertheless, the biodiversity of salt mines associated with biotechnological potential has not been well characterized. The present study paper examines the biodiversity of microorganisms in the Bochnia Salt Mine based on 16S rRNA gene and shotgun sequencing. Biodiversity studies revealed a significantly higher relative abundance of Chlamydiae at the first level of the mine (3.5%) compared to the other levels (< 0.1%). Patescibacteria microorganisms constituted a high percentage (21.6%) in the sample from site RA6. Shotgun sequencing identified 16 unique metagenome-assembled genomes (MAGs). Although one was identified as Halobacterium bonnevillei, the others have not yet been assigned to any species; it is possible that these species may be undescribed. Preliminary analyses of the biotechnological and pharmaceutical potential of microorganisms inhabiting the mine were also performed, and the biosynthetic gene cluster (BGC) profiles and antimicrobial peptide (AMP) coding genes in individual samples were characterized. Hundreds of BGCs and dozens of AMP coding genes were identified in metagenomes. Our findings indicate that Polish salt mines are promising sites for further research aimed at identifying microorganisms that are producers of potentially important substances with biotechnological and pharmaceutical applications.

Landfill leachate treatment by a combination of a multiple plant hybrid constructed wetland system with a solar photoFenton process in a raceway pond reactor

The sustainable and green treatment of landfill leachate (LL), produced by municipal solid waste, represents one of the most relevant challenges in the integrated waste management systems. Accordingly, in this work a green solution was investigated by coupling an innovative hybrid constructed wetland (HCW) to a solar photo-Fenton (SPF) process. A multiple layers HCW pilot plant including different medium substrates (sand, solid compost and carriers) and plant species (Phragmites australis, Arundo donax and A. plinii) was designed. The HCW was functionalised with compost tea solution to simultaneously provide high nutrient content for plants and increase the microorganism biodiversity. Process efficiency was investigated using different real LLs (young and mature) in terms of chemical oxygen demand (COD), nitrogen compounds, chlorides and metals. Removals in the range 75–95% were observed for all the parameters after ten days of leachate recirculation in the pilot plant. Subsequently, the SPF process was carried out in a raceway pond reactor (RPR) as polishing step, significantly improving COD removal (further 49%). HCW combined with SPF in RPR would allow to meet the corresponding limits according to the final use/fate of the effluent by modulating the main parameters of the process.

Practical value of microorganisms for forensic purposes (on the example of microbial flora of bony remnants from the historic burial site)

Phenotypic signs of dominants isolated from the surface of bony remnants from the historic burial site were analyzed in order to expand data on the biodiversity of microorganisms in the microbial flora of bony remnants and to assess the possibility of using the results of microbiological analysis in the evidence base of forensic examination and forensic archaeology. It was detected that only Deuteromycota and Eubacteria colonized all types of surfaces in the samples of bone fragments from the historic burial site (with the age in the range of 90-95 years); with the abundance of micromycetes, the proportion of Eubacteria naturally decreased, while with the increased bacterial background counts the rate of micromycetes detection decreased. The insignificant amount of nutrients in the bony remnants led to the decrease in the number and biological diversity of microorganisms contaminating them; species adapted to a hard-to-reach organic substrate dominated there. During the process of bony remnants decomposition, when the conditions of their location changed, inter-species competition and specific recolonization occurred by species of microorganisms most adapted to a hard-to-reach organic substrate in the abiotic and biotic conditions of existence given. The results obtained are important for the descriptive ecology and biology of specific groups of microorganisms in the postmortem microbiome and form the basis for a more thorough study of complex communications between species of microorganisms in the necrobiome of bony remnants - in the future it will allow putting forward original hypotheses about the involvement of microbes in the circulation of matter and energy, as well as to apply the information obtained in the evidence base of forensic examination and forensic archaeology.

Determination of Anoxygenic Photosynthetic Bacteria from Water and Sediment in Dumai Coastal Water, Indonesia

Dumai is one of the coastal waters of Indonesia that has the potential for the biodiversity of microorganisms including anoxygenic photosynthetic bacteria (APB). Anoxygenic photosynthetic bacteria are bacteria that carry out decomposition activities even though oxygen levels in water and sediment are very little or even absent. This study aims to determine anoxygenic photosynthetic bacteria from aquatic and sedimentary ecosystems in the coastal waters of Dumai, Indonesia. This research was conducted by an experimental method using modified mineral media. The APB was isolated from six different places in sequence, namely Dumai sea station, river prayer room, harbor, shrimp pond area, fish auction place, and, Purnama tour. All bacteria obtained were then characterized by their morphological and physiological characteristics. The isolation results showed that 15 different bacterial isolates were obtained after being determined based on Bergey’s Manual of Determinative Bacteriology. All isolates contained different pigments such as carotenoids, xanthophylls, and, chlorophylls. Thus, further utilization of APB bacteria can be carried out in various microbiological applications such as bioremediation, aquaculture, biofuel, food, and medicines.

Changes in Soil Biological Properties after Sewage Sludge and Pesticide Application in Wheat Cultivation

One of the solutions implemented in order to improve the quality of soils exposed to pesticides is the application of sewage sludge, which is a by-product of wastewater treatment. As an organic substrate, it provides soil with important nutrients, such as nitrogen and phosphorus, and enriches it with organic matter, thanks to which it can be a valuable fertilizer. The aim of the presented research was to evaluate the influence of granulated sewage sludge (GSS) on the biological properties of soil treated with herbicides (MCPA and dicamba) and fungicides (thiophanate-methyl and azoxystrobin). The following aspects were investigated: the activity of selected soil enzymes, the genetic biodiversity of bacteria and fungi, and the abundance of the bacterial gene responsible for ammonia oxidation. A field experiment was conducted, in which granulated sewage sludge (GSS) was applied to soil at a single dose of 3 t/ha. Wheat (Triticum aestivum L.) was sown on the prepared plots. The herbicides (H) and fungicides (F) as well as their mixture (F + H) were applied to the plants in the appropriate growth phases in the doses recommended by the producer. The control was soil without sewage sludge (C). The samples taken were tested for: dehydrogenases, catalases and urease activities, genetic biodiversity structure of bacteria and fungi by TRFLP assay, and the abundance of the bacterial amoA gene by qPCR. On the basis of the obtained results, it was found that the application of pesticides to soil fertilized with sewage sludge influenced the enzymatic activity of soil, and their activity differed depending on the tested enzyme. The activity of URE and DHA on the plots with GSS was higher by approx. 20% and 30%, respectively, as compared to the plots without GSS application. Moreover, both the genetic biodiversity of microorganisms and the abundance of amoA gene differed depending on the variant of the experiment. The GSS treatment of soil significantly influenced the growth of the studied gene as compared to C, and its abundance was 9.15 log10 gene copies/g DW of soil. Due to the content of nutrients in sewage sludge, it can be a valuable fertilizer in agricultural crops treated with pesticides.

Effect of Environmental Heterogeneity and Trophic Status in Sampling Strategy on Estimation of Small-Scale Regional Biodiversity of Microorganisms.

Microorganisms are diverse and play key roles in lake ecosystems, therefore, a robust estimation of their biodiversity and community structure is crucial for determining their ecological roles in lakes. Conventionally, molecular surveys of microorganisms in lakes are primarily based on equidistant sampling. However, this sampling strategy overlooks the effects of environmental heterogeneity and trophic status in lake ecosystems, which might result in inaccurate biodiversity assessments of microorganisms. Here, we conducted equidistant sampling from 10 sites in two regions with different trophic status within East Lake (Wuhan, China), to verify the reliability of this sampling strategy and assess the influence of environmental heterogeneity and trophic status on this strategy. Rarefaction curves showed that the species richness of microbial communities in the region of the lake with higher eutrophication failed to reach saturation compared with that in lower trophic status. The microbial compositions of samples from the region with higher trophic status differed significantly (P < 0.05) from those in the region with lower trophic status. The result of this pattern may be explained by complex adaptations of lake microorganisms in high eutrophication regions with environmental conditions, where community differentiation can be viewed as adaptations to these environmental selection forces. Therefore, when conducting surveys of microbial biodiversity in a heterogeneous environment, investigators should incorporate intensive sampling to assess the variability in microbial distribution in response to a range of factors in the local microenvironment.

Батыс Қазақстан кен орындарының мұнайпласт суларынан оқшауланған микроорганизмдердің таксономиялық әртүрлілігін шетелдік мұнай кен орындарымен салыстыру

The article describes a variety of microorganisms, isolated from oil reservoir waters of different oilfields that are main objects in studying the micrоbiаl еnhаnсеd оil rесоvеrу (МЕОR) methods. Microorganisms can generate a number of potentially useful metabolites (biomass, biosurfactants, bioacid, biosolvents, biopolymer, biogas) for oil recovery. These metabolites help to reduce the oil’s viscosity and the interfacial friction between oil and water as a surfactant, increase its porosity and permeability. The article discusses the taxonomic biodiversity of microorganisms of oil-formation waters of three active wells of the “Zhetybai”, “Kulsary”, and “Akingen” fields and from different oil deposits across the world for several years. The significance of oil microorganisms, their research, the importance of MEOR processes, comparison of oil microbes between international and Western Kazakhstan oil reserves and future of these microorganisms are widely studied. The article provides information on microorganisms, such as Bacillus sp., Pseudomonas sp., that are more immune to adverse shifts in environmental changes. These genera produce surfactants, gases, alcohols, acids, and biopolymers. The similarity of the taxonomic biodiversity of oil microorganisms of oilfields in Western Kazakhstan and their prospects, as well as the use of microorganisms from the distant countries’ oilfields in the MEOR processes are analyzed.

Soil from Serianthes Rhizosphere Influences Growth and Leaf Nutrient Content of Serianthes Plants

Soils from the rhizosphere of perennial plants accumulate microorganisms that influence the growth of other plants. This microorganism biodiversity may be exploited by using these soils as an inoculum in new planting sites. Soils collected from the rhizosphere of mature Serianthes trees were subjected to treatments designed to reduce or increase microorganism populations, then were used in a series of five studies to grow Serianthes plants in container culture. Serianthes kanehirae and Serianthes grandiflora stem growth was 14–19% greater, leaf nitrogen was 40–46% greater, leaf phosphorus was 50–86% greater, and leaf potassium was 28–43% greater when grown in soils from Serianthes rhizosphere than in soils away from a Serianthes tree. Treating the Serianthes rhizosphere soils with sterilization or propiconazole fungicide reduced stem growth of S. grandiflora, S. kanehirae, and Serianthes nelsonii plants by 16–47% below that of untreated soils. The sterilization and fungicide treatments also consistently reduced phosphorus (48–50%) and potassium (12–21%) content of leaves when compared with untreated rhizosphere soil. Adding Rhizophagus irregularis inoculum to the sterilized soil reversed the reduction in S. grandiflora stem growth and leaf phosphorus content. These findings indicate that soils from the Serianthes rhizosphere contain beneficial microorganisms for Serianthes plant growth and leaf nutritional status and exploiting these soils as an inoculum for new planting sites may provide a net-positive influence on post-transplant growth and survival.

Microbial Communities in Biocrusts Are Recruited From the Neighboring Sand at Coastal Dunes Along the Baltic Sea.

Biological soil crusts occur worldwide as pioneer communities stabilizing the soil surface. In coastal primary sand dunes, vascular plants cannot sustain due to scarce nutrients and the low-water-holding capacity of the sand sediment. Thus, besides planted dune grass, biocrusts are the only vegetation there. Although biocrusts can reach high coverage rates in coastal sand dunes, studies about their biodiversity are rare. Here, we present a comprehensive overview of the biodiversity of microorganisms in such biocrusts and the neighboring sand from sampling sites along the Baltic Sea coast. The biodiversity of Bacteria, Cyanobacteria, Fungi, and other microbial Eukaryota were assessed using high-throughput sequencing (HTS) with a mixture of universal and group-specific primers. The results showed that the biocrusts recruit their microorganisms mainly from the neighboring sand rather than supporting a universal biocrust microbiome. Although in biocrusts the taxa richness was lower than in sand, five times more co-occurrences were identified using network analysis. This study showed that by comparing neighboring bare surface substrates with biocrusts holds the potential to better understand biocrust development. In addition, the target sequencing approach helps outline potential biotic interactions between different microorganisms groups and identify key players during biocrust development.

ENVIRONMENTAL RISKS OF MICRO-CONTAMINATION OF THE ENVIRONMENT WITH TETRACYCLINE

Review of environmental risks associated with the use of tetracycline. Micro-contamination with tetracycline has both medical risks associated with the manifestation of antibiotic resistance in bacterial communities, and environmental risks associated with changes in the transformation of substances in ecosystems and the impact on biodiversity by inhibiting certain species of plants, animals and microorganisms.Micro-contamination with tetracycline antibiotics entails a number of environmental risks. Due to the widespread use, the spread of tetracycline antibiotics in the environment has a global scale. The effect of tetracycline is observed in many objects. The spread of tetracycline is promoted by veterinary use, both directly and as a result of the use of animal waste as fertilizers for agricultural crops and pastures. As a result of the study, the following possible environmental consequences of micro-contamination of the environment with tetracycline were identified:1. Disruption of the work of bacteria included in the bacterial complex of activated sludge at sewage treatment plants using this technology, as well as during composting and affecting the processes of denitrification;2. Impacts on soil microbial communities by suppressing a number of processes of substance biodegradation and changing the biodiversity of microorganisms;3. The risks of micro-contamination of plant communities with tetracycline coming from organic fertilizers are associated with the inhibition of a number of root nutrition processes, species-specific for different crops;4. Microcontamination of marine communities with tetracycline is primarily associated with the impact on producers - algae and cyanobacteria, inhibiting their growth. And secondly, to the subsequent food chains by bioaccumulation in the tissues of vertebrates;5. The toxic effect of small doses of tetracycline from the soil on certain invertebrate species has been shown.

Effects of short-term space conditions on cellulose degradation ability and biodiversity of microorganisms

Effects of short-term space conditions on cellulose degradation ability and biodiversity of microorganisms

Overview of regional‐scale diversity patterns of freshwater algae in a Neotropical bromeliad ecosystem

Abstract A large part of freshwater microorganism biodiversity is contained in the bromeliad ecosystem of the Neotropics, which form a multitude of small islands in a terrestrial matrix. While aquatic communities of bromeliads and their food‐web organisation are relatively well documented, processes that shape diversity in such small water bodies remain largely understudied. Based on 217 bromeliad ecosystems from six sites located in French Guiana, we determined the factors that shape the diversity pattern of algal communities. We considered a broad range of environmental and ecological variables, including canopy openness, habitat characteristics, and invertebrate biomass, to identify the main drivers of algal community structure and biodiversity across bromeliads in a c. 25,000 km2 region. We found no evidence of random distribution or spatial structuring of algal communities. Algal biomass was mainly influenced by habitat size and complexity, particulate organic matter content, and light energy, while algal richness was primarily controlled by habitat size. Change in community structure as habitat size increases was driven by species turnover with increasing proportion of filamentous taxa. Our results indicate that, due to the large diversity of aquatic habitats they provide at a small spatial scale, bromeliads are critical ecosystems sustaining freshwater microorganism biodiversity.