scholarly journals Soil properties and sulfur-oxidizing bacterial diversity in response to different planting patterns of shallot (Allium ascalonicum)

2020 ◽  
Vol 21 (6) ◽  
Author(s):  
Muhammad Juwanda ◽  
SAKHIDIN ◽  
SAPARSO ◽  
KHARISUN
Keyword(s):  
Soil Properties ◽  
Bacterial Diversity ◽  
Burkholderia Cepacia ◽  
Dry Season ◽  
Rrna Gene ◽  
Rice Soil ◽  
Klebsiella Aerogenes ◽  
Bacterial Strains ◽  
Organic C ◽  
Sulfur Oxidizing

Abstract. Juwanda M, Sakhidin, Saparso, Kharisun. 2020. Soil properties and sulfur-oxidizing bacterial diversity in response to different planting patterns of shallot (Allium ascalonicum). Biodiversitas 21: 2832-2839. Sulfur is one of the primary elements required by plants for growth and development. Sulfur-oxidizing bacteria (SOB) can oxidize sulfur to sulfate, which is directly taken up by plant roots. This study aims to evaluate the soil properties and SOB diversity in various shallot planting patterns, i.e. PP1 (shallot-dry season-shallot-shallot), PP2 (shallot-dry season-shallot-rice), and PP3 (shallot-pulses-shallot-rice). Soil samples were collected from the rhizosphere of the shallot plant and analyzed for the soil properties based on the standard methods. Bacteria isolation was cultured on Starkey broth and Starkey agar. Bacteria isolate was identified based on the 16S rRNA gene sequence and compared to the GenBank database. The results showed that shallot planting patterns influence soil properties and SOB diversity. The highest content of sulfate (41.31 ppm), organic C (0.957 %), organic matter (1.650%), C/N ratio (9.57), and SOB diversity was obtained in PP3 planting pattern. Three bacterial strains have been successfully isolated i.e. A-3245D, B-3246F, and C-3247C with their closest related to Burkholderia cepacia, Klebsiella variicola, and Klebsiella aerogenes, respectively. The highest diversity and population density of SOB was in the PP3 planting patterns, i.e Burkholderia cepacia (7.45 x 105 CFU/mL); Klebsiella variicola (1.79 x 107 CFU/mL; Klebsiella aerogenes: 3.9 x 106 CFU/mL). K. variicola can be found in three planting patterns of shallot.

scholarly journals Isolation and Characterization of a Sulfur-Oxidizing Chemolithotroph Growing on Crude Oil under Anaerobic Conditions

2003 ◽  
Vol 69 (1) ◽  
pp. 107-112 ◽  
Author(s):  
Yumiko Kodama ◽  
Kazuya Watanabe
Keyword(s):  
Crude Oil ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Anaerobic Conditions ◽  
Molecular Approaches ◽  
Oil Storage ◽  
Isolation And Characterization ◽  
Inorganic Medium ◽  
Sulfur Oxidizing ◽  
Microaerobic Conditions

ABSTRACT Molecular approaches have shown that a group of bacteria (called cluster 1 bacteria) affiliated with the ε subclass of the class Proteobacteria constituted major populations in underground crude-oil storage cavities. In order to unveil their physiology and ecological niche, this study isolated bacterial strains (exemplified by strain YK-1) affiliated with the cluster 1 bacteria from an oil storage cavity at Kuji in Iwate, Japan. 16S rRNA gene sequence analysis indicated that its closest relative was Thiomicrospira denitrificans (90% identity). Growth experiments under anaerobic conditions showed that strain YK-1 was a sulfur-oxidizing obligate chemolithotroph utilizing sulfide, elemental sulfur, thiosulfate, and hydrogen as electron donors and nitrate as an electron acceptor. Oxygen also supported its growth only under microaerobic conditions. Strain YK-1 could not grow on nitrite, and nitrite was the final product of nitrate reduction. Neither sugars, organic acids (including acetate), nor hydrocarbons could serve as carbon and energy sources. A typical stoichiometry of its energy metabolism followed an equation: S2− + 4NO3 − → SO4 2− + 4NO2 − (ΔG 0 = −534 kJ mol−1). In a difference from other anaerobic sulfur-oxidizing bacteria, this bacterium was sensitive to NaCl; growth in medium containing more than 1% NaCl was negligible. When YK-1 was grown anaerobically in a sulfur-depleted inorganic medium overlaid with crude oil, sulfate was produced, corresponding to its growth. On the contrary, YK-1 could not utilize crude oil as a carbon source. These results suggest that the cluster 1 bacteria yielded energy for growth in oil storage cavities by oxidizing petroleum sulfur compounds. Based on its physiology, ecological interactions with other members of the groundwater community are discussed.

scholarly journals High Culturable Bacterial Diversity From a European Desert: The Tabernas Desert

2021 ◽  
Vol 11 ◽  
Author(s):  
Esther Molina-Menor ◽  
Helena Gimeno-Valero ◽  
Javier Pascual ◽  
Juli Peretó ◽  
Manuel Porcar
Keyword(s):  
New Species ◽  
Bacterial Diversity ◽  
Ecological Niches ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Comprehensive Strategy ◽  
Simple Strategy ◽  
Large Numbers ◽  
Environmental Bacteria ◽  
Bacterial Biodiversity

One of the most diverse ecological niches for microbial bioprospecting is soil, including that of drylands. Drylands are one of the most abundant biomes on Earth, but extreme cases, such as deserts, are considered very rare in Europe. The so-called Tabernas Desert is one of the few examples of a desert area in continental Europe, and although some microbial studies have been performed on this region, a comprehensive strategy to maximize the isolation of environmental bacteria has not been conducted to date. We report here a culturomics approach to study the bacterial diversity of this dryland by using a simple strategy consisting of combining different media, using serial dilutions of the nutrients, and using extended incubation times. With this strategy, we were able to set a large (254 strains) collection of bacteria, the majority of which (93%) were identified through 16S ribosomal RNA (rRNA) gene amplification and sequencing. A significant fraction of the collection consisted of Actinobacteria and Proteobacteria, as well as Firmicutes strains. Among the 254 isolates, 37 different genera were represented, and a high number of possible new taxa were identified (31%), of which, three new Kineococcus species. Moreover, 5 out of the 13 genera represented by one isolate were also possible new species. Specifically, the sequences of 80 isolates held a percentage of identity below the 98.7% threshold considered for potentially new species. These strains belonged to 20 genera. Our results reveal a clear link between medium dilution and isolation of new species, highlight the unexploited bacterial biodiversity of the Tabernas Desert, and evidence the potential of simple strategies to yield surprisingly large numbers of diverse, previously unreported, bacterial strains and species.

Bacterial diversity of soil samples from the western Himalayas, India

2009 ◽  
Vol 55 (5) ◽  
pp. 564-577 ◽  
Author(s):  
Pooja Gangwar ◽  
Syed Imteyaz Alam ◽  
Sunita Bansod ◽  
Lokendra Singh
Keyword(s):  
Bacterial Diversity ◽  
Bacterial Species ◽  
Hydrolytic Enzymes ◽  
Soil Samples ◽  
Rrna Gene ◽  
Organic Carbon Content ◽  
Western Himalayas ◽  
Bacterial Strains ◽  
Culture Independent ◽  
The One

High-altitude cold habitats of the Himalayas are little explored with respect to bacterial diversity. Diverse bacterial species and phylotypes obtained by culture-dependent and culture-independent approaches are reported here. Phylogenetic analysis and modulation of bacterial diversity with altitude and available organic carbon content are also described. Psychrophilic and psychrotolerant bacteria dominated the Himalayan habitats, accounting for 60% of the cultivated strains. Isolates produced one or more (up to five) hydrolytic enzymes, lipase being the one secreted by most strains (62%). Partial 16S rRNA gene sequences were obtained for 99 bacterial strains and 74 clones obtained from soil samples from the western Himalayas. Forty-five percent of cultured bacterial strains belonged to the Proteobacteria group with 39% belonging to γ-Proteobacteria. Firmicutes was the second most abundant class with 32% of the total isolates followed by Actinobacteria (16%) and Bacteroidetes (6%). Most of the strains belonged to the genus Bacillus (30%) followed by Pseudomonas (24%) and Arthrobacter (12%). In culture-independent studies, phylotypes belonging to the Proteobacteria were dominant (73%) with the majority being β-Proteobacteria (31%). The bacterial diversity exhibited an altitude gradient with a gradual decline in the number of genera with increase in altitude. The isolates exhibited close phylogenetic affinities to bacteria from other cold habitats.

scholarly journals Highly parallelized microfluidic droplet cultivation and prioritization on antibiotic producers from complex natural microbial communities

2019 ◽  
Author(s):  
Lisa Mahler ◽  
Sarah Niehs ◽  
Karin Martin ◽  
Thomas Weber ◽  
Kirstin Scherlach ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Natural Products ◽  
Bacterial Diversity ◽  
High Throughput ◽  
High Throughput Screening ◽  
Single Cells ◽  
Amplicon Sequencing ◽  
Droplet Microfluidics ◽  
Rrna Gene ◽  
Bacterial Strains

AbstractTo investigate the overwhelming part of the bacterial diversity still evading standard cultivation for its potential use in antibiotic synthesis, we have compiled a microscale-cultivation and screening system. We devised a strategy based on droplet-microfluidics taking advantage of the inherent miniaturization and high throughput. Single cells of natural samples were confined in 9 x 106 aqueous droplets and subjected to long-term incubation under controlled conditions. Subsequent a high-throughput screening for antimicrobial natural products was implemented, employing a whole cell reporting system using the viability of reporter strains as a probe for antimicrobial activity. Due to the described microscale cultivation a novel subset of bacterial strains was made available for the following screening for antimicrobials. We demonstrate the merits of the in-droplet cultivation by comparing the cultivation outcome in microfluidic droplets and on conventional agar plates for a bacterial community derived from soil by 16S rRNA gene amplicon sequencing. In-droplet cultivation resulted in a significantly higher bacterial diversity without the common overrepresentation of Firmicutes. Natural strains able to inhibit either a Gram-positive or a Gram-negative reporter strain were isolated from the microscale system and further cultivated. Thereby a variety of rare isolates was obtained. The natural products with antimicrobial activity were elucidated for the most promising candidate. Our method combines a new cultivation approach with a high-throughput search for antibiotic producers to increase the chances of finding new lead substances.

scholarly journals Plant Growth Modifications Due to Coastal Embankments Affect Soil Bacterial and Archaeal Communities Over the Growing Season in Salt Marshes of Eastern China

2022 ◽  
Author(s):  
Hongyu Feng ◽  
Yajun Qiao ◽  
Lu Xia ◽  
Wen Yang ◽  
Yongqiang Zhao ◽  
...  
Keyword(s):  
Salt Marsh ◽  
Microbial Diversity ◽  
Soil Properties ◽  
Salt Marshes ◽  
Soil Nutrient ◽  
Rrna Gene ◽  
Organic C ◽  
Bacterial And Archaeal Communities ◽  
Soil Bacterial ◽  
Archaeal Communities

Abstract Aims: Although the influences of coastal embankments on physicochemical soil properties and carbon (C) and nitrogen (N) cycling have been widely studied, the mechanisms of their effects on soil microbial ecologies remain poorly understood. Thus, the aim of this study was to investigate variations in the diversity and composition of soil bacterial and archaeal communities between natural and embanked saltmarshes, as well as the determinants that drive these variations.Methods: 16S rRNA gene sequence analysis was performed to assess the impacts of embankments on the bacterial and archaeal communities of native Suaeda salsa, Phragmites australis, and invasive Spartina alterniflora saltmarshes on the east coast of China.Results: Embankments were found to significantly decrease the microbial diversity of the S. alterniflora salt marsh, while they increased the OTU richness of the P. australis salt marsh. Embankments modified the compositions of soil bacterial and archaeal communities in both the S. alterniflora and P. australis salt marshes. However, variations in the microbial diversity, richness, and community compositions between the native and embanked S. salsa salt marshes were insignificant. Conclusions: These results were possibly because the embankment significantly altered soil nutrient substrate levels (e.g., soil organic C and N) by variations in plant residues and physiochemical soil properties in S. alterniflora and P. australis saltmarshes, whereas the embankment had no observable changes in the soil nutrient substrate and the plant residue in S. salsa saltmarsh. This study also elucidated the effects of coastal embankments on biogeochemical cycles, and highlighted their potential hazards to ecosystems.

scholarly journals Combined Effect of Laboratory-Simulated Fire and Chromium Pollution on Microbial Communities in an Agricultural Soil

Biology ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 587
Author(s):  
Ida Rascio ◽  
Maddalena Curci ◽  
Concetta Eliana Gattullo ◽  
Anna Lavecchia ◽  
Mohammad Yaghoubi Khanghahi ◽  
...  
Keyword(s):  
Soil Properties ◽  
Microbial Communities ◽  
Relative Abundance ◽  
Agricultural Soil ◽  
Crop Residues ◽  
Soil Microbial Communities ◽  
Soil Conditions ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Soil Microbial

Fire events in agricultural soils can modify not only soil properties but also the structure of soil microbial communities, especially in soils containing high concentrations of potentially toxic elements (PTEs). The recolonization of burned soils can in fact favor the proliferation of certain microorganisms, more adaptable to post-fire soil conditions and higher PTE availability, over others. In this study, we simulated with laboratory experiments the microbial recolonization of an agricultural soil containing high Cr concentrations after heating at 500 °C for 30 min, to mimic the burning of crop residues. Changes in soil properties and Cr speciation were assessed, as well as soil microbial structure by means of 16S rRNA gene sequencing. Both altered soil conditions and increased Cr availability, especially Cr(VI), appeared to be responsible for the reduction in species diversity in heated soils and the proliferation of Firmicutes. Indeed, already after 3 days from the heat treatment, Firmicutes increased from 14% to 60% relative abundance. In particular, Paenibacillus was the most abundant genus identified after the simulation, with an average relative abundance of 40%. These bacteria are known to be good fire-responders and Cr-tolerant. These results could be useful to identify bacterial strains to be used as bioindicators of altered environments and for the recovery of fire-impacted polluted sites.

DIVERSITY OF CULTURABLE BACTERIAL MICROBIOTA OF THE Eisenia foetida DIGESTIVE TRACT

2018 ◽  
Vol 41 (3) ◽  
pp. 255-264 ◽  
Author(s):  
J. Abraham Pérez-Pérez ◽  
David Espinosa-Victoria ◽  
Hilda V. Silva-Rojas ◽  
Lucía López-Reyes
Keyword(s):  
Bacterial Diversity ◽  
Digestive Tract ◽  
Bacterial Species ◽  
Brain Heart Infusion ◽  
Rrna Gene ◽  
Eisenia Foetida ◽  
Bacterial Isolates ◽  
Bacterial Microbiota ◽  
Decomposition Of Organic Matter ◽  
Earthworm Gut

Bacteria are an unavoidable component of the natural earthworm diet; thus, bacterial diversity in the earthworm gut is directly linked to decomposition of organic matter and development of the surrounding plants. The aim of this research was to isolate and to identify biochemically and molecularly the culturable bacterial microbiota of the digestive tract of Eisenia foetida. Earthworms were sourced from Instituto de Reconversión Productiva y Bioenergética (IRBIO) and Colegio de Postgraduados (COLPOS), México. Bacterial isolation was carried out on plates of Brain Heart Infusion (BHI) culture medium. Fifty six and 44 bacterial isolates were obtained from IRBIO and COLPOS, respectively. The population was composed of 44 Gram-negative and 56 Gram-positive isolates. Over 50 % of the bacterial isolates were rod-shaped cells. The 16S rRNA gene was sequenced and nine genera were identified in worms from IRBIO (Bacillus, Paenibacillus, Solibacillus, Staphylococcus, Arthrobacter, Pantoea, Stenotrophomonas, Acinetobacter and Aeromonas) and six in worms from COLPOS (Bacillus, Paenibacillus, Stenotrophomonas, Staphylococcus, Acinetobacter and Aeromonas). Bacillus was the predominant genus, with eight and six species in the oligochaetes from IRBIO and COLPOS, respectively. The most represented bacteria in the worms from both sites were Bacillus sp. and B. subtilis. The predominance of Bacillus was probably due to spore formation, a reproductive strategy that ensures survival and dispersion in the soil and oligochaetes digestive tract. The gut of E. foetida not only harbored bacterial species of agronomic importance but also species potentially pathogenic for humans (Staphylococcus warneri, Pantoea agglomerans and Stentrophomonas sp.). The larger bacterial diversity in worms from IRBIO could be due to their feeding on cattle manure, which is a rich source of bacteria.

Corrigendum to: Conservation agriculture effects on soil properties and crop productivity in a semiarid region of India

Soil Research ◽  
2019 ◽  
Vol 57 (2) ◽  
pp. 200 ◽  
Author(s):  
J. Somasundaram ◽  
M. Salikram ◽  
N. K. Sinha ◽  
M. Mohanty ◽  
R. S. Chaudhary ◽  
...  
Keyword(s):  
Soil Properties ◽  
Management Practices ◽  
Crop Yields ◽  
Cropping Systems ◽  
Soil Layer ◽  
Conservation Agriculture ◽  
Semiarid Region ◽  
Reduced Tillage ◽  
Organic C ◽  
Residue Retention

Conservation agriculture (CA) including reduced or no-tillage and crop residue retention, is known to be a self–sustainable system as well as an alternative to residue burning. The present study evaluated the effect of reduced tillage coupled with residue retention under different cropping systems on soil properties and crop yields in a Vertisol of a semiarid region of central India. Two tillage systems – conventional tillage (CT) with residue removed, and reduced tillage (RT) with residue retained – and six major cropping systems of this region were examined after 3 years of experimentation. Results demonstrated that soil moisture content, mean weight diameter, percent water stable aggregates (>0.25mm) for the 0–15cm soil layer were significantly (Pmoderately labile>less labile. At the 0–15cm depth, the contributions of moderately labile, less labile and non-labile C fractions to total organic C were 39.3%, 10.3% and 50.4% respectively in RT and corresponding values for CT were 38.9%, 11.7% and 49.4%. Significant differences in different C fractions were observed between RT and CT. Soil microbial biomass C concentration was significantly higher in RT than CT at 0–15cm depth. The maize–chickpea cropping system had significantly (P–1 followed by soybean+pigeon pea (2:1) intercropping (3.50 t ha–1) and soybean–wheat cropping systems (2.97 t ha–1). Thus, CA practices could be sustainable management practices for improving soil health and crop yields of rainfed Vertisols in these semiarid regions.

scholarly journals Campylobacter insulaenigrae bacteremia with meningitis: a case report

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Moe Kyotani ◽  
Tsuneaki Kenzaka ◽  
Hozuka Akita ◽  
Soichi Arakawa
Keyword(s):  
Blood Culture ◽  
Marine Mammals ◽  
Chronic Subdural Hematoma ◽  
16S Rrna Gene Sequencing ◽  
Enhancement Effect ◽  
Rrna Gene ◽  
Clinical Report ◽  
Bacterial Strains ◽  
Fisher Syndrome ◽  
First Case

Abstract Background The bacterium Campylobacter insulaenigrae was first isolated from marine mammals of Scotland in 2004. Only one case of C. insulaenigrae infection in humans has been previously reported. Case presentation An 89-year-old Japanese man without dementia was admitted to our hospital, because he presented with a fever of 38 °C and weakness in right leg since 5 days. He had organized chronic subdural hematoma (CSH), and no history of pre-infection. At the time of admission, he had paralysis of the extraocular muscle, ataxia, and low manual muscle test score of the right side. He was suspected to have Miller Fisher syndrome; however, these symptoms improved without any treatment. On day 22 in the hospital, the patient presented a fever of 38.8 °C, left cranial nerve disorder, and hemiplegia. On day 25, the patient presented with signs of meningeal irritation; cerebrospinal fluid examination indicated an increase in the number of apocytes and a low glucose level. A contrast magnetic resonance imaging (MRI) scan of the patient’s head indicated a contrast enhancement effect in his right meninges. The blood culture showed presence of spirillums; 16S rRNA gene sequencing confirmed that the spirillums in the blood culture were Campylobacter insulaenigrae (C. insulaenigrae). We started treatment with meropenem for bacteremia and meningitis. When the symptoms improved, meropenem was replaced with ampicillin, based on the result of the drug sensitivity test. The treatment continued for 4 weeks. Conclusions We report the first case of meningitis caused by C. insulaenigrae bacteremia in humans, and the second clinical report of C. insulaenigrae infection in humans. The bacterial strains isolated from humans and marine mammals had different genotypes. This suggests that different genotypes could be responsible for differences in the hosts. Further case studies are needed to establish the reasons behind the difference in the manifestations of C. insulaenigrae infections reported so far.

scholarly journals Microbiome of Odontogenic Abscesses

2021 ◽  
Vol 9 (6) ◽  
pp. 1307
Author(s):  
Sebastian Böttger ◽  
Silke Zechel-Gran ◽  
Daniel Schmermund ◽  
Philipp Streckbein ◽  
Jan-Falco Wilbrand ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Oral Microbiome ◽  
Minor Role ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Bacterial Strains ◽  
16S Rrna Gene Analysis ◽  
Odontogenic Infections ◽  
Odontogenic Abscess

Severe odontogenic abscesses are regularly caused by bacteria of the physiological oral microbiome. However, the culture of these bacteria is often prone to errors and sometimes does not result in any bacterial growth. Furthermore, various authors found completely different bacterial spectra in odontogenic abscesses. Experimental 16S rRNA gene next-generation sequencing analysis was used to identify the microbiome of the saliva and the pus in patients with a severe odontogenic infection. The microbiome of the saliva and the pus was determined for 50 patients with a severe odontogenic abscess. Perimandibular and submandibular abscesses were the most commonly observed diseases at 15 (30%) patients each. Polymicrobial infections were observed in 48 (96%) cases, while the picture of a mono-infection only occurred twice (4%). On average, 31.44 (±12.09) bacterial genera were detected in the pus and 41.32 (±9.00) in the saliva. In most cases, a predominantly anaerobic bacterial spectrum was found in the pus, while saliva showed a similar oral microbiome to healthy individuals. In the majority of cases, odontogenic infections are polymicrobial. Our results indicate that these are mainly caused by anaerobic bacterial strains and that aerobic and facultative anaerobe bacteria seem to play a more minor role than previously described by other authors. The 16S rRNA gene analysis detects significantly more bacteria than conventional methods and molecular methods should therefore become a part of routine diagnostics in medical microbiology.

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