Bacterial succession and metabolite changes during flax (Linum usitatissimum L.) retting with Bacillus cereus HDYM-02.

PubMed

Zhao, Dan; Liu, Pengfei; Pan, Chao; Du, Renpeng; Ping, Wenxiang; Ge, Jingping

2016-09-02

High-throughput sequencing and GC-MS (gas chromatography-mass spectrometry) were jointly used to reveal the bacterial succession and metabolite changes during flax (Linum usitatissimum L.) retting. The inoculation of Bacillus cereus HDYM-02 decreased bacterial richness and diversity. This inoculum led to the replacement of Enterobacteriaceae by Bacillaceae. The level of aerobic Pseudomonadaceae (mainly Azotobacter) and anaerobic Clostridiaceae_1 gradually increased and decreased, respectively. Following the addition of B. cereus HDYM-02, the dominant groups were all degumming enzyme producers or have been proven to be involved in microbial retting throughout the entire retting period. These results could be verified by the metabolite changes, either degumming enzymes or their catalytic products galacturonic acid and reducing sugars. The GC-MS data showed a clear separation between flax retting with and without B. cereus HDYM-02, particularly within the first 72 h. These findings reveal the important bacterial groups that are involved in fiber retting and will facilitate improvements in the retting process.

Effect of pig manure on the chemical composition and microbial diversity during co-composting with spent mushroom substrate and rice husks.

PubMed

Meng, Xingyao; Liu, Bin; Xi, Chen; Luo, Xiaosha; Yuan, Xufeng; Wang, Xiaofen; Zhu, Wanbin; Wang, Hongliang; Cui, Zongjun

2018-03-01

In this study, the impact of pig manure on the maturity of compost consisting of spent mushroom substrate and rice husks was accessed. The results showed that the addition of pig manure (SMS-PM) reached 50°C 5days earlier and lasted 15days longer than without pig manure (SMS). Furthermore, the addition of pig manure improved nutrition and germination index. High-throughput 16S rRNA pyrosequencing was used to evaluate the bacterial and fungal composition during the composting process of SMS-PM compared to SMS alone. The SMS treatment showed a relatively higher abundance of carbon-degrading microbes (Bacillaceae and Thermomyces) and plant pathogenic fungi (Sordariomycetes_unclassified) at the end of the compost. In contrast, the SMS-PM showed an increased bacterial diversity with anti-pathogen (Pseudomonas). The results indicated that the addition of pig manure improved the decomposition of refractory carbon from the spent mushroom substrate and promoted the maturity and nutritional content of the compost product. Copyright © 2017. Published by Elsevier Ltd.

Phylogenetic position of the North American isolate of Pasteuria that parasitizes the soybean cyst nematode, Heterodera glycines, as inferred from 16S rDNA sequence analysis.

PubMed

Atibalentja, N; Noel, G R; Domier, L L

2000-03-01

A 1341 bp sequence of the 16S rDNA of an undescribed species of Pasteuria that parasitizes the soybean cyst nematode, Heterodera glycines, was determined and then compared with a homologous sequence of Pasteuria ramosa, a parasite of cladoceran water fleas of the family Daphnidae. The two Pasteuria sequences, which diverged from each other by a dissimilarity index of 7%, also were compared with the 16S rDNA sequences of 30 other bacterial species to determine the phylogenetic position of the genus Pasteuria among the Gram-positive eubacteria. Phylogenetic analyses using maximum-likelihood, maximum-parsimony and neighbour-joining methods showed that the Heterodera glycines-infecting Pasteuria and its sister species, P. ramosa, form a distinct line of descent within the Alicyclobacillus group of the Bacillaceae. These results are consistent with the view that the genus Pasteuria is a deeply rooted member of the Clostridium-Bacillus-Streptococcus branch of the Gram-positive eubacteria, neither related to the actinomycetes nor closely related to true endospore-forming bacteria.

Common Virulence Factors and Tissue Targets of Entomopathogenic Bacteria for Biological Control of Lepidopteran Pests

PubMed Central

Castagnola, Anaïs; Stock, S. Patricia

2014-01-01

This review focuses on common insecticidal virulence factors from entomopathogenic bacteria with special emphasis on two insect pathogenic bacteria Photorhabdus (Proteobacteria: Enterobacteriaceae) and Bacillus (Firmicutes: Bacillaceae). Insect pathogenic bacteria of diverse taxonomic groups and phylogenetic origin have been shown to have striking similarities in the virulence factors they produce. It has been suggested that the detection of phage elements surrounding toxin genes, horizontal and lateral gene transfer events, and plasmid shuffling occurrences may be some of the reasons that virulence factor genes have so many analogs throughout the bacterial kingdom. Comparison of virulence factors of Photorhabdus, and Bacillus, two bacteria with dissimilar life styles opens the possibility of re-examining newly discovered toxins for novel tissue targets. For example, nematodes residing in the hemolymph may release bacteria with virulence factors targeting neurons or neuromuscular junctions. The first section of this review focuses on toxins and their context in agriculture. The second describes the mode of action of toxins from common entomopathogens and the third draws comparisons between Gram positive and Gram negative bacteria. The fourth section reviews the implications of the nervous system in biocontrol. PMID:24634779

Acute, sublethal, and combination effects of azadirachtin and Bacillus thuringiensis on the cotton bollworm, Helicoverpa armigera

PubMed Central

Abedi, Zahra; Saber, Moosa; Vojoudi, Samad; Mahdavi, Vahid; Parsaeyan, Ehsan

2014-01-01

Abstract The cotton bollworm, Helicoverpa armigera Hübner (Lepidoptera: Noctuidae) is a polyphagous and cosmopolitan insect pest that causes damage to various plants. In this study, the lethal and sublethal effects of azadirachtin and Bacillus thuringiensis Berliner sub sp . kurstaki (Bacillales: Bacillaceae) were evaluated on third instar H. armigera under laboratory conditions. The LC50 values of azadirachtin and Bt were 12.95 and 96.8 µg a.i./mL, respectively. A total mortality of 56.7% was caused on third instar larvae when LC20 values of the insecticides were applied in combination with each other. The LT50 values of azadirachtin and Bt were 4.8 and 3.6 days, respectively. The results of the sublethal study showed that the application of LC30 value of azadirachtin and Bt reduced the larval and pupal weight and increased larval and pupal duration of H. armigera . The longevity and fecundity of female adults were affected significantly by the insecticides. Female fecundity was reduced by the treatments, respectively. The lowest adult emergence ratio and pupation ratio were observed in the azadirachtin treatment. The results indicated that both insecticides have high potential for controlling of the pest. PMID:25373177

[Community structure and diversity of culturable moderate halophilic bacteria isolated from Qrhan salt lake on Qinghai-Tibet Plateau].

PubMed

Shen, Shuo

2017-04-04

I studied the community structure and diversity of culturable moderate halophilic bacteria isolated from Qrhan Salt Lake. I isolated and cultured the moderate halophilic bacteria on different selective media. After the 16S rRNA gene sequences was amplified and measured, I constructed the phylogenic tree, analyzed the community structure and calculated the diversity indexes according to the 16S rRNA gene information. A total of 421 moderate halophilic bacteria were isolated from water and mud samples in Qrhan Salt Lake. The 16S rRNA gene information showed that 4 potential novel species belonged to the family Bacillaceae. Eighty-three model strains belonged to 3 phylurms 6 families 16 genus. Among them, Bacillus sp., Oceanobacillus sp. and Halomonas sp. were dominant species. Diversity analysis showed that the diversity of strains isolated from water sample was higher than that from mud sample, but the dominance degree of strains isolated from mud sample was higher than that from water sample. The genetic diversity of moderate halophilic bacteria isolated from Qrhan Salt Lake was abundant. Also, there were dominant and novel species of culturable moderate halophilic bacteria in this lake.

Quantifying the biases in metagenome mining for realistic assessment of microbial ecology of naturally fermented foods.

PubMed

Keisam, Santosh; Romi, Wahengbam; Ahmed, Giasuddin; Jeyaram, Kumaraswamy

2016-09-27

Cultivation-independent investigation of microbial ecology is biased by the DNA extraction methods used. We aimed to quantify those biases by comparative analysis of the metagenome mined from four diverse naturally fermented foods (bamboo shoot, milk, fish, soybean) using eight different DNA extraction methods with different cell lysis principles. Our findings revealed that the enzymatic lysis yielded higher eubacterial and yeast metagenomic DNA from the food matrices compared to the widely used chemical and mechanical lysis principles. Further analysis of the bacterial community structure by Illumina MiSeq amplicon sequencing revealed a high recovery of lactic acid bacteria by the enzymatic lysis in all food types. However, Bacillaceae, Acetobacteraceae, Clostridiaceae and Proteobacteria were more abundantly recovered when mechanical and chemical lysis principles were applied. The biases generated due to the differential recovery of operational taxonomic units (OTUs) by different DNA extraction methods including DNA and PCR amplicons mix from different methods have been quantitatively demonstrated here. The different methods shared only 29.9-52.0% of the total OTUs recovered. Although similar comparative research has been performed on other ecological niches, this is the first in-depth investigation of quantifying the biases in metagenome mining from naturally fermented foods.

Bacterium-bacterium inhibitory interactions among psychrotrophic bacteria isolated from Antarctic seawater (Terra Nova Bay, Ross Sea).

PubMed

Lo Giudice, Angelina; Brilli, Matteo; Bruni, Vivia; De Domenico, Maria; Fani, Renato; Michaud, Luigi

2007-06-01

One hundred and forty bacteria isolated from Antarctic seawater samples were examined for their ability to inhibit the growth of indigenous isolates and their sensitivity to antibacterial activity expressed by one another. On the basis of 16S rRNA gene sequencing and analysis, bacterial isolates were assigned to five phylogenetically different taxa, Actinobacteria, alpha and gamma subclasses of Proteobacteria, Bacillaceae, and Bacteroidetes. Twenty-one isolates (15%), predominantly Actinobacteria, exhibited antagonistic properties against marine bacteria of Antarctic origin. Members of Bacteroidetes and Firmicutes did not show any inhibitory activity. Differences were observed among inhibition patterns of single isolates, suggesting that their activity was more likely strain-specific rather than dependent on phylogenetic affiliation. A novel analysis based on network theory confirmed these results, showing that the structure of this population is probably robust to perturbations, but also that it depends strongly on the most active strains. The determination of plasmid incidence in the bacterial strains investigated revealed that there was no correlation between their presence and the antagonistic activity. The data presented here provide evidence for the antagonistic interactions within bacterial strains inhabiting Antarctic seawater and suggest the potential exploitation of Antarctic bacteria as a novel source of antibiotics.

Viable bacterial population and persistence of foodborne pathogens on the pear carpoplane.

PubMed

Duvenage, Francois J; Duvenage, Stacey; Du Plessis, Erika M; Volschenk, Quinton; Korsten, Lise

2017-03-01

Knowledge on the culturable bacteria and foodborne pathogen presence on pears is important for understanding the impact of postharvest practices on food safety assurance. Pear fruit bacteria were investigated from the point of harvest, following chlorine drenching and after controlled atmosphere (CA) storage to assess the impact on natural bacterial populations and potential foodborne pathogens. Salmonella spp. and Listeria monocytogenes were detected on freshly harvested fruit in season one. During season one, chemical drenching and CA storage did not have a significant effect on the bacterial load of orchard pears, except for two farms where the populations were lower 'after CA storage'. During season two, bacterial populations of orchard pears from three of the four farms increased significantly following drenching; however, the bacterial load decreased 'after CA storage'. Bacteria isolated following enumeration included Enterobacteriaceae, Microbacteriaceae, Pseudomonadaceae and Bacillaceae, with richness decreasing 'after drench' and 'after CA storage'. Salmonella spp. and L. monocytogenes were not detected after postharvest practices. Postharvest practices resulted in decreased bacterial species richness. Understanding how postharvest practices have an impact on the viable bacterial populations of pear fruit will contribute to the development of crop-specific management systems for food safety assurance. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Antimicrobial activities of novel cultivable bacteria isolated from marine sponge Tedania anhelans

NASA Astrophysics Data System (ADS)

Zeng, Zhen; Zhao, Jing; Ke, Caihuan; Wang, Dexiang

2013-05-01

Marine sponge Tedania anhelans distributes throughout the intertidal zone of Fujian, southeastern China, and is a potential source of natural bioactive products. The sponge harbors a large number of bacterial groups that have been identified using various techniques, including fluorescent in situ hybridization (FISH). Fractionation of dissociated sponge allowed isolation of 25 bacterial species. Based on 16S rRNA gene sequencing, phylogenetic analysis attributed most of these eubacteria to α- Proteobacteria, γ- Proteobacteria, Cytophaga / Flavobacterium / Bacteroidetes (CFB group), and the family Bacillaceae of Gram-positive bacteria. In sequence similarity, five putatively novel species were identified with less than 98% similarity to other strains in the NCBI database. Tests for antimicrobial activities were performed against Gram-positive bacteria, Gram-negative bacteria, fungi, antitumor indicators Escherichia coli 343/591 (with DNA repair deficiency), regular E. coli 343/636 (with different DNA repair capacity), and 10 bacterial isolates exhibited inhibitory bioactivities. Among these strains, three isolates were detected involving function gene NRPS-A domains, which were most closely related to the amino acid sequences of linear gramicidin synthetase and pyoverdine synthetase. These results contribute to our knowledge of the microbes associated with marine sponges and further reveal novel bacterial resources for the screening of bioactive marine natural products.

Global transcriptomic response of Anoxybacillus sp. SK 3-4 to aluminum exposure.

PubMed

Lim, Jia Chun; Thevarajoo, Suganthi; Selvaratnam, Chitra; Goh, Kian Mau; Shamsir, Mohd Shahir; Ibrahim, Zaharah; Chong, Chun Shiong

2017-02-01

Anoxybacillus sp. SK 3-4 is a Gram-positive, rod-shaped bacterium and a member of family Bacillaceae. We had previously reported that the strain is an aluminum resistant thermophilic bacterium. This is the first report to provide a detailed analysis of the global transcriptional response of Anoxybacillus when the cells were exposed to 600 mg L -1 of aluminum. The transcriptome was sequenced using Illumina MiSeq sequencer. Total of 708 genes were differentially expressed (fold change >2.00) with 316 genes were up-regulated while 347 genes were down-regulated, in comparing to control with no aluminum added in the culture. Based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the majority of genes encoding for cell metabolism such as glycolysis, sulfur metabolism, cysteine and methionine metabolism were up-regulated; while most of the gene associated with tricarboxylic acid cycle (TCA cycle) and valine, leucine and isoleucine metabolism were down-regulated. In addition, a significant number of the genes encoding ABC transporters, metal ions transporters, and some stress response proteins were also differentially expressed following aluminum exposure. The findings provide further insight and help us to understand on the resistance of Anoxybacillus sp. SK 3-4 toward aluminium. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Microbial composition of the Korean traditional food "kochujang" analyzed by a massive sequencing technique.

PubMed

Nam, Young-Do; Park, So-lim; Lim, Seong-Il

2012-04-01

Kochujang is a traditional Korean fermented food that is made with red pepper, glutinous rice, salt, and soybean. Kochujang is fermented by naturally occurring microorganisms through which it obtains various health-promoting properties. In this study, the bacterial diversities of 9 local and 2 commercial brands of kochujang were analyzed with a barcoded pyrosequencing technique targeting the hyper-variable regions V1/V2 of the 16S rRNA gene. Through the analysis of 13524 bacterial pyrosequences, 223 bacterial species were identified, most of which converged on the phylum Firmicutes (average 93.1%). All of the kochujang samples were largely populated (>90.9% of abundance) by 12 bacterial families, and Bacillaceae showed the highest abundance in all but one sample. Bacillus subtilis and B. licheniformis were the most dominant bacterial species and were broadly distributed among the kochujang samples. Each sample contained a high abundance of region-specific bacterial species, such as B. sonorensis, B. pumilus, Weissella salipiscis, and diverse unidentified Bacillus species. Phylotype- and phylogeny-based community comparison analysis showed that the microbial communities of the two commercial brands were different from those of the local brands. Moreover, each local brand kochujang sample had region-specific microbial community reflecting the manufacturing environment. © 2012 Institute of Food Technologists®

Streptohalobacillus salinus gen. nov., sp. nov., a moderately halophilic, Gram-positive, facultative anaerobe isolated from subsurface saline soil.

PubMed

Wang, Xiaowei; Xue, Yanfen; Ma, Yanhe

2011-05-01

A Gram-stain-positive, rod-shaped, non-sporulating, motile and moderately halophilic bacterium, designated strain H96B60(T), was isolated from a saline soil sample of the Qaidam basin, China. The strain was facultatively anaerobic. Major end products formed from glucose fermentation were acetate, ethanol and lactic acid. The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The isoprenoid quinone component was menaquinone-6 (MK-6). The predominant cellular fatty acids were C(16: 0), anteiso-C(13 : 0) and anteiso-C(15 : 0). The genomic DNA G+C content of strain H96B60(T) was 36.2 mol%. Phylogenetic analysis based on comparative 16S rRNA gene sequences indicated that strain H96B60(T) represented a novel phyletic lineage within the family Bacillaceae and was related most closely to Halolactibacillus species (96.1-96.4 % similarity). Based on the phenotypic, chemotaxonomic and phylogenetic data presented, strain H96B60(T) is considered to represent a novel species of a new genus, for which the name Streptohalobacillus salinus gen. nov., sp. nov. is proposed. The type strain of Streptohalobacillus salinus is H96B60(T) ( = DSM 22440(T)  = CGMCC 1.7733(T)).

Influence of resistance breeding in common bean on rhizosphere microbiome composition and function.

PubMed

Mendes, Lucas William; Raaijmakers, Jos M; de Hollander, Mattias; Mendes, Rodrigo; Tsai, Siu Mui

2018-01-01

The rhizosphere microbiome has a key role in plant growth and health, providing a first line of defense against root infections by soil-borne pathogens. Here, we investigated the composition and metabolic potential of the rhizobacterial community of different common bean (Phaseolus vulgaris) cultivars with variable levels of resistance to the fungal root pathogen Fusarium oxysporum (Fox). For the different bean cultivars grown in two soils with contrasting physicochemical properties and microbial diversity, rhizobacterial abundance was positively correlated with Fox resistance. Pseudomonadaceae, bacillaceae, solibacteraceae and cytophagaceae were more abundant in the rhizosphere of the Fox-resistant cultivar. Network analyses showed a modular topology of the rhizosphere microbiome of the Fox-resistant cultivar, suggesting a more complex and highly connected bacterial community than in the rhizosphere of the Fox-susceptible cultivar. Metagenome analyses further revealed that specific functional traits such as protein secretion systems and biosynthesis genes of antifungal phenazines and rhamnolipids were more abundant in the rhizobacterial community of the Fox-resistant cultivar. Our findings suggest that breeding for Fox resistance in common bean may have co-selected for other unknown plant traits that support a higher abundance of specific beneficial bacterial families in the rhizosphere with functional traits that reinforce the first line of defense.

Conductive iron oxide minerals accelerate syntrophic cooperation in methanogenic benzoate degradation.

PubMed

Zhuang, Li; Tang, Jia; Wang, Yueqiang; Hu, Min; Zhou, Shungui

2015-08-15

Recent studies have suggested that conductive iron oxide minerals can facilitate syntrophic metabolism of the methanogenic degradation of organic matter, such as ethanol, propionate and butyrate, in natural and engineered microbial ecosystems. This enhanced syntrophy involves direct interspecies electron transfer (DIET) powered by microorganisms exchanging metabolic electrons through electrically conductive minerals. Here, we evaluated the possibility that conductive iron oxides (hematite and magnetite) can stimulate the methanogenic degradation of benzoate, which is a common intermediate in the anaerobic metabolism of aromatic compounds. The results showed that 89-94% of the electrons released from benzoate oxidation were recovered in CH4 production, and acetate was identified as the only carbon-bearing intermediate during benzoate degradation. Compared with the iron-free controls, the rates of methanogenic benzoate degradation were enhanced by 25% and 53% in the presence of hematite and magnetite, respectively. This stimulatory effect probably resulted from DIET-mediated methanogenesis in which electrons transfer between syntrophic partners via conductive iron minerals. Phylogenetic analyses revealed that Bacillaceae, Peptococcaceae, and Methanobacterium are potentially involved in the functioning of syntrophic DIET. Considering the ubiquitous presence of iron minerals within soils and sediments, the findings of this study will increase the current understanding of the natural biological attenuation of aromatic hydrocarbons in anaerobic environments. Copyright © 2015 Elsevier B.V. All rights reserved.

Platinum Recovery from Synthetic Extreme Environments by Halophilic Bacteria.

PubMed

Maes, Synthia; Props, Ruben; Fitts, Jeffrey P; Smet, Rebecca De; Vilchez-Vargas, Ramiro; Vital, Marius; Pieper, Dietmar H; Vanhaecke, Frank; Boon, Nico; Hennebel, Tom

2016-03-01

Metal recycling based on urban mining needs to be established to tackle the increasing supply risk of critical metals such as platinum. Presently, efficient strategies are missing for the recovery of platinum from diluted industrial process streams, often characterized by extremely low pHs and high salt concentrations. In this research, halophilic mixed cultures were employed for the biological recovery of platinum (Pt). Halophilic bacteria were enriched from Artemia cysts, living in salt lakes, in different salt matrices (sea salt mixture and NH4Cl; 20-210 g L(-1) salts) and at low to neutral pH (pH 3-7). The main taxonomic families present in the halophilic cultures were Halomonadaceae, Bacillaceae, and Idiomarinaceae. The halophilic cultures were able to recover >98% Pt(II) and >97% Pt(IV) at pH 2 within 3-21 h (4-453 mg Ptrecovered h(-1) g(-1) biomass). X-ray absorption spectroscopy confirmed the reduction to Pt(0) and transmission electron microscopy revealed both intra- and extracellular Pt precipitates, with median diameters of 9-30 nm and 11-13 nm, for Pt(II) and Pt(IV), respectively. Flow cytometric membrane integrity staining demonstrated the preservation of cell viability during platinum recovery. This study demonstrates the Pt recovery potential of halophilic mixed cultures in acidic saline conditions.

Diversity of Bacillus-like bacterial community in the sediments of the Bamenwan mangrove wetland in Hainan, China.

PubMed

Liu, Min; Cui, Ying; Chen, Yuqing; Lin, Xiangzhi; Huang, Huiqin; Bao, Shixiang

2017-03-01

Members of the genus Bacillus and related spore-forming genera are ubiquitous. However, Bacillus-like species isolated from marine sediments have attracted less interest than their terrestrial relatives. Here, we investigated the diversity of Bacillus-like bacterial communities in the sediments of the Bamenwan mangrove wetland in Hainan, China, using culture-dependent and culture-independent methods, and present the first report on this subject. We also discovered some potential novel species from the sediment samples. Four families, Bacillaceae (58%), Paenibacillaceae (22%), Alicyclobacillaceae (15%), and Planococcaceae (5%), and 9 genera, Bacillus (42%), Paenibacillus (16%), Halobacillus (13%), Alicyclobacillus (11%), Rummeliibacillus (5%), Cohnella (5%), Tumebacillus (4%), Pontibacillus (3%), and Aneurinibacillus (2%), were identified by pyrosequencing. In contrast, only 4 genera, Bacillus (57%), Paenibacillus (23%), Halobacillus (14%), and Virgibacillus (6%), were detected by the culture-dependent method. In the 16S rDNA sequencing analysis, the isolates HB12036 and HB12037 were closest to Bacillus okuhidensis Kh10-101 T and Paenibacillus xylanilyticus XIL14 T with similarities of 94.8% and 95.9%, respectively, indicating that these were novel species. Bacillus sp. HB12035 and HB12040 exhibited antimicrobial activity against Staphylococcus aureus ATCC 25923, and Bacillus sp. HB12033 exhibited antimicrobial activity against Ustilago scitaminea Syd.

Sediminibacillus massiliensis sp. nov., a moderately halophilic, Gram-positive bacterium isolated from a stool sample of a young Senegalese man.

PubMed

Senghor, Bruno; Bassène, Hubert; Khelaifia, Saber; Robert, Catherine; Fournier, Pierre-Edouard; Ruimy, Raymond; Sokhna, Cheikh; Raoult, Didier; Lagier, Jean-Christophe

2018-07-01

A Gram-positive, moderately halophilic bacterium, referred to as strain Marseille-P3518 T , was isolated from a stool sample with 2% NaCl concentration from a healthy 15-year-old male living in Dielmo, a village in Senegal. Cells are aerobic, rod-shaped and motile and display endospore formation. Strain Marseille-P3518 T can grow in a medium with 0-20% (w/v) sodium chloride (optimally at 5-7.5% w/v). The major fatty acids were 12-methyl-tetradecanoic acid (45.8%), 13-methyl-tetradecanoic acid (26.9%) and 12-methyl-tridecanoic acid (12.8%). The genome is 4,347,479 bp long with 42.1% G+C content. It contains 4282 protein-coding and 107 RNA genes. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that strain Marseille-P3518 T is a member of the Bacillaceae family and is closely related to Sediminibacillus albus (97.4% gene sequence similarity). Strain Marseille-P3518 T was clearly differentiated from its phylogenetic neighbors on the basis of phenotypic and genotypic features. Strain Marseille-P3518 T is, therefore, considered to be a novel representative of the genus Sediminibacillus, for which the name Sediminibacillus massiliensis sp. nov. is proposed, and the type strain is Marseille-P3518 T (CSUR P3518T, DSM69894).

Biodegradation of insensitive munition formulations IMX101 and IMX104 in surface soils.

PubMed

Indest, Karl J; Hancock, Dawn E; Crocker, Fiona H; Eberly, Jed O; Jung, Carina M; Blakeney, Gary A; Brame, Jon; Chappell, Mark A

2017-07-01

The biodegradation potential of insensitive munition melt cast formulations IMX101 and IMX104 was investigated in two unamended training range soils under aerobic and anaerobic growth conditions. Changes in community profiles in soil microcosms were monitored via high-throughput 16S rRNA sequencing over the course of the experiments to infer key microbial phylotypes that may be linked to IMX degradation. Complete anaerobic biotransformation occurred for IMX101 and IMX104 constituents 2,4-dinitroanisole (DNAN) and 3-nitro-1,2,4-triazol-5-one during the 30-day incubation period with Camp Shelby (CS) soil. By comparison, soil from Umatilla chemical depot demonstrated incomplete DNAN degradation with reduced transformation rates for both IMX101 and IMX104. Aerobic soil microcosms for both soils demonstrated reduced transformation rates compared to anaerobic degradation for all IMX constituents with DNAN the most susceptible to biotransformation by CS soil. Overall, IMX constituents hexahydro-1,3,5-trinitro-1,3,5-triazine and 1-nitroguanidine did not undergo significant transformation. In CS soil, organisms that have been associated with explosives degradation, namely members of the Burkholderiaceae, Bacillaceae, and Paenibacillaceae phylotypes increased significantly in anaerobic treatments whereas Sphingomonadaceae increased significantly in aerobic treatments. Collectively, these data may be used to populate fate and transport models to provide more accurate estimates for assessing environmental costs associated with release of IMX101 and IMX104.

Microbial hitchhikers on intercontinental dust: catching a lift in Chad

PubMed Central

Favet, Jocelyne; Lapanje, Ales; Giongo, Adriana; Kennedy, Suzanne; Aung, Yin-Yin; Cattaneo, Arlette; Davis-Richardson, Austin G; Brown, Christopher T; Kort, Renate; Brumsack, Hans-Jürgen; Schnetger, Bernhard; Chappell, Adrian; Kroijenga, Jaap; Beck, Andreas; Schwibbert, Karin; Mohamed, Ahmed H; Kirchner, Timothy; de Quadros, Patricia Dorr; Triplett, Eric W; Broughton, William J; Gorbushina, Anna A

2013-01-01

Ancient mariners knew that dust whipped up from deserts by strong winds travelled long distances, including over oceans. Satellite remote sensing revealed major dust sources across the Sahara. Indeed, the Bodélé Depression in the Republic of Chad has been called the dustiest place on earth. We analysed desert sand from various locations in Chad and dust that had blown to the Cape Verde Islands. High throughput sequencing techniques combined with classical microbiological methods showed that the samples contained a large variety of microbes well adapted to the harsh desert conditions. The most abundant bacterial groupings in four different phyla included: (a) Firmicutes—Bacillaceae, (b) Actinobacteria—Geodermatophilaceae, Nocardiodaceae and Solirubrobacteraceae, (c) Proteobacteria—Oxalobacteraceae, Rhizobiales and Sphingomonadaceae, and (d) Bacteroidetes—Cytophagaceae. Ascomycota was the overwhelmingly dominant fungal group followed by Basidiomycota and traces of Chytridiomycota, Microsporidia and Glomeromycota. Two freshwater algae (Trebouxiophyceae) were isolated. Most predominant taxa are widely distributed land inhabitants that are common in soil and on the surfaces of plants. Examples include Bradyrhizobium spp. that nodulate and fix nitrogen in Acacia species, the predominant trees of the Sahara as well as Herbaspirillum (Oxalobacteraceae), a group of chemoorganotrophic free-living soil inhabitants that fix nitrogen in association with Gramineae roots. Few pathogenic strains were found, suggesting that African dust is not a large threat to public health. PMID:23254516

Bioprospecting for secondary metabolites in the entomopathogenic bacterium Photorhabdus luminescens subsp. sonorensis.

PubMed

Orozco, Rousel A; Molnár, István; Bode, Helge; Stock, S Patricia

2016-11-01

Crude extracts of in vitro and in vivo cultures of two strains of Photorhabdus l. sonorensis (Enterobacteriaceae) were analyzed by TLC, HPLC-UV and LC-MS. Nine unique compounds with mass/charge ratios (m/z) ranging from 331.3 to 713.5 were found in MS analyses. Bioactivity of extracts was assessed on a selection of plant pathogens/pests and non-target species. Caborca strain extracts showed the highest activity against Helicoverpa zea (Lepidoptera: Noctuidae) neonates at all concentrations tested. Mortality ranged from 11% (at 10μg/ml) to 37% (at 40μg/ml). Strain CH35 extracts showed the highest nematicidal activity on Meloidogyne incognita (Tylenchida: Meloidogynidae) at 40μg/ml. Low to no nematicidal activity was observed against the non-target species Steinernema carpocapsae (Rhabditida: Steinernematidae) and Caenorhabditis elegans (Rhabditida: Rhabditidae). Caborca extracts exhibited a strong antibiotic effect on Pseudomonas syringae (Pseudomonadales: Pseudomonadacedae) at 40μg/ml, while both Caborca and CH35 extracts inhibited the growth of Bacillus subitillis (Bacillales: Bacillaceae) at 40μg/ml. All extracts strongly inhibited the growth of the fungus Fusarium oxysporum (Hypocreales: Nectriceae) but not that of Alternaria alternata (Pleosporales: Pleosporaceae). Contrastingly, a moderate to high inhibitory effect was denoted on the non-target biocontrol fungus Beauveria bassiana (Hypocreales: Clavivipitaceae). Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

Diversity, Bacterial Symbionts and Antibacterial Potential of Gut-Associated Fungi Isolated from the Pantala flavescens Larvae in China

PubMed Central

Shao, Ming-Wei; Lu, Yi-Hui; Miao, Shuang; Zhang, Yun; Chen, Ting-Ting; Zhang, Ying-Lao

2015-01-01

The diversity of fungi associated with the gut of Pantala flavescens larvae was investigated using a culture-dependent method and molecular identification based on an analysis of the internally transcribed spacer sequence. In total, 48 fungal isolates were obtained from P. flavescens larvae. Based on phylogenetic analyses, the fungal isolates were grouped in 5 classes and 12 different genera. Fourteen bacterial 16S rDNA sequences derived from total genomic DNA extractions of fungal mycelia were obtained. The majority of the sequences were associated with Proteobacteria (13/14), and one Bacillaceae (1/14) was included. Leclercia sp., Oceanobacillus oncorhynchi and Methylobacterium extorquens, were reported for the first time as bacterial endosymbionts in fungi. High-performance liquid chromatography (HPLC) analysis indicated that bacterial symbionts produced specific metabolites and also exerted an inhibitory effect on fungal metabolites. The biological activity of the fungal culture extracts against the pathogenic bacteria Staphylococcus aureus (ATCC 6538), Bacillus subtilis (ATCC 6633) and Escherichia coli (ATCC 8739) was investigated, and 20 extracts (42%) exhibited antibacterial activity against at least one of the tested bacterial strains. This study is the first report on the diversity and antibacterial activity of symbiotic fungi residing in the gut of P. flavescens larvae, and the results show that these fungi are highly diverse and could be exploited as a potential source of bioactive compounds. PMID:26221957

Diversity, Bacterial Symbionts and Antibacterial Potential of Gut-Associated Fungi Isolated from the Pantala flavescens Larvae in China.

PubMed

Shao, Ming-Wei; Lu, Yi-Hui; Miao, Shuang; Zhang, Yun; Chen, Ting-Ting; Zhang, Ying-Lao

2015-01-01

The diversity of fungi associated with the gut of Pantala flavescens larvae was investigated using a culture-dependent method and molecular identification based on an analysis of the internally transcribed spacer sequence. In total, 48 fungal isolates were obtained from P. flavescens larvae. Based on phylogenetic analyses, the fungal isolates were grouped in 5 classes and 12 different genera. Fourteen bacterial 16S rDNA sequences derived from total genomic DNA extractions of fungal mycelia were obtained. The majority of the sequences were associated with Proteobacteria (13/14), and one Bacillaceae (1/14) was included. Leclercia sp., Oceanobacillus oncorhynchi and Methylobacterium extorquens, were reported for the first time as bacterial endosymbionts in fungi. High-performance liquid chromatography (HPLC) analysis indicated that bacterial symbionts produced specific metabolites and also exerted an inhibitory effect on fungal metabolites. The biological activity of the fungal culture extracts against the pathogenic bacteria Staphylococcus aureus (ATCC 6538), Bacillus subtilis (ATCC 6633) and Escherichia coli (ATCC 8739) was investigated, and 20 extracts (42%) exhibited antibacterial activity against at least one of the tested bacterial strains. This study is the first report on the diversity and antibacterial activity of symbiotic fungi residing in the gut of P. flavescens larvae, and the results show that these fungi are highly diverse and could be exploited as a potential source of bioactive compounds.

Volatilization and precipitation of tellurium by aerobic, tellurite-resistant marine microbes.

PubMed

Ollivier, Patrick R L; Bahrou, Andrew S; Marcus, Sarah; Cox, Talisha; Church, Thomas M; Hanson, Thomas E

2008-12-01

Microbial resistance to tellurite, an oxyanion of tellurium, is widespread in the biosphere, but the geochemical significance of this trait is poorly understood. As some tellurite resistance markers appear to mediate the formation of volatile tellurides, the potential contribution of tellurite-resistant microbial strains to trace element volatilization in salt marsh sediments was evaluated. Microbial strains were isolated aerobically on the basis of tellurite resistance and subsequently examined for their capacity to volatilize tellurium in pure cultures. The tellurite-resistant strains recovered were either yeasts related to marine isolates of Rhodotorula spp. or gram-positive bacteria related to marine strains within the family Bacillaceae based on rRNA gene sequence comparisons. Most strains produced volatile tellurides, primarily dimethyltelluride, though there was a wide range of the types and amounts of species produced. For example, the Rhodotorula spp. produced the greatest quantities and highest diversity of volatile tellurium compounds. All strains also produced methylated sulfur compounds, primarily dimethyldisulfide. Intracellular tellurium precipitates were a major product of tellurite metabolism in all strains tested, with nearly complete recovery of the tellurite initially provided to cultures as a precipitate. Different strains appeared to produce different shapes and sizes of tellurium containing nanostructures. These studies suggest that aerobic marine yeast and Bacillus spp. may play a greater role in trace element biogeochemistry than has been previously assumed, though additional work is needed to further define and quantify their specific contributions.

Microbial control of phytophagous invertebrate pests in South Africa: Current status and future prospects.

PubMed

Hatting, Justin L; Moore, Sean D; Malan, Antoinette P

2018-02-07

Invertebrate pests pose a significant threat to food security on the African continent. In response, South Africa has become one of the largest importers of chemical pesticides in sub-Saharan Africa, with several hundred active ingredients registered. To address the over-reliance on such chemicals, the South African Department of Agriculture, Forestry and Fisheries (DAFF) has eliminated or restricted several pesticides since the late 1970s. The recent launch of the South African National Bio-Economy Strategy and establishment of the South African Bioproducts Organisation (SABO), together with new guidelines for registration of biopesticides in 2015, also support this endeavour. Concurrently, entomopathogen-related research and bioproduct development has increased over the past decade. Currently, 31 products (seven manufactured locally) are registered under the Fertilizers, Farm Feeds, Agricultural Remedies and Stock Remedies Act 36 of 1947. Commercially important microbes include Beauveria bassiana (Cordycipitaceae), Metarhizium anisopliae (Clavicipitaceae), Cydia pomonella granulovirus, Cryptophlebia leucotreta granulovirus, Helicoverpa armigera nucleopolyhedrovirus (Baculoviridae) and Bacillus thuringiensis subsp. kurstaki and B. thuringiensis subsp. aizawai (Bacillaceae). Both parasitic and entomopathogenic nematodes (EPNs) show potential for development as bioinsecticides with one commercial EPN product, based on Heterorhabditis bacteriophora (Heterorhabditidae), registered under the Act. Rapid scientific progression, supported by a favourable legislative environment, should facilitate further advances in microbial control of phytophagous invertebrate pests in South Africa. Copyright © 2018 Elsevier Inc. All rights reserved.

Acute, sublethal, and combination effects of azadirachtin and Bacillus thuringiensis on the cotton bollworm, Helicoverpa armigera.

PubMed

Abedi, Zahra; Saber, Moosa; Vojoudi, Samad; Mahdavi, Vahid; Parsaeyan, Ehsan

2014-02-26

The cotton bollworm, Helicoverpa armigera Hübner (Lepidoptera: Noctuidae) is a polyphagous and cosmopolitan insect pest that causes damage to various plants. In this study, the lethal and sublethal effects of azadirachtin and Bacillus thuringiensis Berliner sub sp . kurstaki (Bacillales: Bacillaceae) were evaluated on third instar H. armigera under laboratory conditions. The LC50 values of azadirachtin and Bt were 12.95 and 96.8 µg a.i./mL, respectively. A total mortality of 56.7% was caused on third instar larvae when LC20 values of the insecticides were applied in combination with each other. The LT50 values of azadirachtin and Bt were 4.8 and 3.6 days, respectively. The results of the sublethal study showed that the application of LC30 value of azadirachtin and Bt reduced the larval and pupal weight and increased larval and pupal duration of H. armigera. The longevity and fecundity of female adults were affected significantly by the insecticides. Female fecundity was reduced by the treatments, respectively. The lowest adult emergence ratio and pupation ratio were observed in the azadirachtin treatment. The results indicated that both insecticides have high potential for controlling of the pest. This is an open access paper. We use the Creative Commons Attribution 3.0 license that permits unrestricted use, provided that the paper is properly attributed.

Gracilibacillus aidingensis sp. nov., a novel moderately halophilic bacterium isolated from Aiding salt lake.

PubMed

Guan, Tong-Wei; Tian, Lei; Li, En-Yuan; Tang, Shu-Kun; Zhang, Xiao-Ping

2017-11-01

A novel Gram-positive, aerobe, moderately halophilic bacterium was isolated from saline soil of Aiding lake in Xinjiang, north-west of China, designated strain YIM 98001 T . Cells were rod-shaped, motile and grew at 5-20% (w/v) NaCl (optimum 10%), pH 6-10 (optimum pH 7.0) and 4-45 °C (optimum 37 °C). The major cellular fatty acids were anteiso C 15:0 , anteiso C 17:0 , iso C 15:0 . The predominant respiratory quinone was MK-7. Diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid were the major polar lipids. Meso-diaminopimelic acid was the diagnostic diamino acid of the cell-wall peptidoglycan. The G+C content was 36.46 mol%. 16S rRNA gene sequence analysis showed that the strain belongs to the family Bacillaceae, with the highest sequence similarity to the type strain Gracilibacillus thailandensis TP2-8 T (96.84%), followed by Gracilibacillus saliphilus YIM 91119 T (96.78%) and Gracilibacillus ureilyticus MF38 T (96.57%), thus confirming the affiliation of strain YIM 98001 T to the genus Gracilibacillus. The polyphasic approach indicates that strain YIM 98001 T represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus aidingensis is proposed. The type strain is YIM 98001 T (=KCTC 42683 T  = DSMZ 104330 T ).

Isolation, selection and characterization of root-associated growth promoting bacteria in Brazil Pine (Araucaria angustifolia).

PubMed

Ribeiro, Carlos Marcelo; Cardoso, Elke Jurandy Bran Nogueira

2012-01-20

Araucaria angustifolia, a unique species of this genus that occurs naturally in Brazil, has a high socio-economic and environmental value and is critically endangered of extinction, since it has been submitted to intense predatory exploitation during the last century. Root-associated bacteria from A. angustifolia were isolated, selected and characterized for their biotechnological potential of growth promotion and biocontrol of plant pathogenic fungi. Ninety-seven strains were isolated and subjected to chemical tests. All isolates presented at least one positive feature, characterizing them as potential PGPR. Eighteen isolates produced indole-3-acetic acid (IAA), 27 were able to solubilize inorganic phosphate, 21 isolates were presumable diazotrophs, with pellicle formation in nitrogen-free culture medium, 83 were phosphatases producers, 37 were positive for siderophores and 45 endospore-forming isolates were antagonistic to Fusarium oxysporum, a pathogen of conifers. We also observed the presence of bacterial strains with multiple beneficial mechanisms of action. Analyzing the fatty acid methyl ester (FAME) and partial sequencing of the 16S rRNA gene of these isolates, it was possible to characterize the most effective isolates as belonging to Bacillaceae (9 isolates), Enterobacteriaceae (11) and Pseudomonadaceae (1). As far as we know, this is the first study to include the species Ewingella americana as a PGPR. Copyright © 2011 Elsevier GmbH. All rights reserved.

Highly diverse endophytes in roots of Cycas bifida (Cycadaceae), an ancient but endangered gymnosperm.

PubMed

Zheng, Ying; Chiang, Tzen-Yuh; Huang, Chao-Li; Gong, Xun

2018-05-01

As an ancient seed plant, cycads are one of the few gymnosperms that develop a root symbiosis with cyanobacteria, which has allowed cycads to cope with harsh geologic and climatic conditions during the evolutionary process. However, the endophytic microbes in cycad roots remain poorly identified. In this study, using next-generation sequencing techniques, we investigated the microbial diversity and composition of both the coralloid and regular roots of Cycas bifida (Dyer) K.D. Hill. Highly diverse endophytic communities were observed in both the coralloid and regular roots. Of the associated bacteria, the top five families were the Nostocaceae, Sinobacteraceae, Bradyrhizobiaceae, Bacillaceae, and Hyphomicrobiaceae. The Nectriaceae, Trichocomaceae, and Incertae sedis were the predominant fungal families in all root samples. A significant difference in the endophytic bacterial community was detected between coralloid roots and regular roots, but no difference was observed between the fungal communities in the two root types. Cyanobacteria were more dominant in coralloid roots than in regular roots. The divergence of cycad root structures and the modified physiological processes may have contributed to the abundance of cyanobionts in coralloid roots. Consequently, the colonization of cyanobacteria inhibits the assemblage of other endophytes. Our results contribute to an understanding of the species diversity and composition of the cycad-endophyte microbiome and provide an abbreviated list of potential ecological roles of the core microbes present.

Utilisation of Rep-PCR to track microbes in aerosols collected adjacent to their source, a saline lake in Victoria, Australia.

PubMed

Munday, Chris I; O'Loingsigh, Tadhg; Tapper, Nigel J; De Deckker, Patrick; Allison, Gwen E

2013-04-15

Dust storms are a major source of aerosolized bacteria, especially in the drought conditions experienced in Australia in the decade to 2009. The major aims of this project were to identify the culturable bacteria in environmental samples and to genetically fingerprint all isolates using repetitive element PCR (Rep-PCR) to investigate the possibility of tracking isolates from their source into the atmosphere. Four field trips were conducted to a dry lake in western Victoria, Australia to sample aerosols and sediments. Aerosols were collected at heights up to 150 m using vacuum pumps with filters attached to a tethered helium balloon, while corresponding sediments were collected in sterile polypropylene tubes. Isolates were cultivated on Tryptic Soy Agar, R2 Agar and Marine Agar, and grown in dark conditions at ambient temperature. By sequencing the 16S rRNA gene of 270 isolates, fifteen different bacterial families were identified, with both the aerosols and sediments dominated by the Bacillaceae family. Four sets of Rep-PCR primers were tested, with the ERIC and (GTG)5 primers proving to be the most suitable for fingerprinting the cultured taxa. Rep-PCR revealed very high strain diversity in the samples collected, however some strains were still able to be tracked from sediments up to 150 m in height. This shows the potential of Rep-PCR, however very large reference databases would be required for the technique to be more useful. Copyright © 2013 Elsevier B.V. All rights reserved.

Glucokinase contributes to glucose phosphorylation in D-lactic acid production by Sporolactobacillus inulinus Y2-8.

PubMed

Zheng, Lu; Bai, Zhongzhong; Xu, Tingting; He, Bingfang

2012-11-01

Sporolactobacillus inulinus, a homofermentative lactic acid bacterium, is a species capable of efficient industrial D-lactic acid production from glucose. Glucose phosphorylation is the key step of glucose metabolism, and fine-tuned expression of which can improve D-lactic acid production. During growth on high-concentration glucose, a fast induction of high glucokinase (GLK) activity was observed, and paralleled the patterns of glucose consumption and D-lactic acid accumulation, while phosphoenolpyruvate phosphotransferase system (PTS) activity was completely repressed. The transmembrane proton gradient of 1.3-1.5 units was expected to generate a large proton motive force to the uptake of glucose. This suggests that the GLK pathway is the major route for glucose utilization, with the uptake of glucose through PTS-independent transport systems and phosphorylation of glucose by GLK in S. inulinus D-lactic acid production. The gene encoding GLK was cloned from S. inulinus and expressed in Escherichia coli. The amino acid sequence revealed significant similarity to GLK sequences from Bacillaceae. The recombinant GLK was purified and shown to be a homodimer with a subunit molecular mass of 34.5 kDa. Strikingly, it demonstrated an unusual broad substrate specificity, catalyzing phosphorylation of 2-deoxyglucose, mannitol, maltose, galactose and glucosamine, in addition to glucose. This report documented the key step concerning glucose phosphorylation of S. inulinus, which will help to understand the regulation of glucose metabolism and D-lactic acid production.

Volatilization and Precipitation of Tellurium by Aerobic, Tellurite-Resistant Marine Microbes▿ †

PubMed Central

Ollivier, Patrick R. L.; Bahrou, Andrew S.; Marcus, Sarah; Cox, Talisha; Church, Thomas M.; Hanson, Thomas E.

2008-01-01

Microbial resistance to tellurite, an oxyanion of tellurium, is widespread in the biosphere, but the geochemical significance of this trait is poorly understood. As some tellurite resistance markers appear to mediate the formation of volatile tellurides, the potential contribution of tellurite-resistant microbial strains to trace element volatilization in salt marsh sediments was evaluated. Microbial strains were isolated aerobically on the basis of tellurite resistance and subsequently examined for their capacity to volatilize tellurium in pure cultures. The tellurite-resistant strains recovered were either yeasts related to marine isolates of Rhodotorula spp. or gram-positive bacteria related to marine strains within the family Bacillaceae based on rRNA gene sequence comparisons. Most strains produced volatile tellurides, primarily dimethyltelluride, though there was a wide range of the types and amounts of species produced. For example, the Rhodotorula spp. produced the greatest quantities and highest diversity of volatile tellurium compounds. All strains also produced methylated sulfur compounds, primarily dimethyldisulfide. Intracellular tellurium precipitates were a major product of tellurite metabolism in all strains tested, with nearly complete recovery of the tellurite initially provided to cultures as a precipitate. Different strains appeared to produce different shapes and sizes of tellurium containing nanostructures. These studies suggest that aerobic marine yeast and Bacillus spp. may play a greater role in trace element biogeochemistry than has been previously assumed, though additional work is needed to further define and quantify their specific contributions. PMID:18849455

Impact of Corn Earworm (Lepidoptera: Noctuidae) on Field Corn (Poales: Poaceae) Yield and Grain Quality.

PubMed

Bibb, Jenny L; Cook, Donald; Catchot, Angus; Musser, Fred; Stewart, Scott D; Leonard, Billy Rogers; Buntin, G David; Kerns, David; Allen, Tom W; Gore, Jeffrey

2018-05-28

Corn earworm, Helicoverpa zea (Boddie), commonly infests field corn, Zea mays (L.). The combination of corn plant biology, corn earworm behavior in corn ecosystems, and field corn value renders corn earworm management with foliar insecticides noneconomical. Corn technologies containing Bacillus thuringiensis (Bt) Berliner (Bacillales: Bacillaceae) were introduced that exhibit substantial efficacy against corn earworm and may reduce mycotoxin contamination in grain. The first generation Bt traits in field corn demonstrated limited activity on corn earworm feeding on grain. The pyramided corn technologies have greater cumulative protein concentrations and higher expression throughout the plant, so these corn traits should provide effective management of this pest. Additionally, reduced kernel injury may affect physical grain quality. Experiments were conducted during 2011-2012 to investigate corn earworm impact on field corn yield and grain quality. Treatments included field corn hybrids expressing the Herculex, YieldGard, and Genuity VT Triple Pro technologies. Supplemental insecticide treatments were applied every 1-2 d from silk emergence until silk senescence to create a range of injured kernels for each technology. No significant relationship between the number of corn earworm damaged kernels and yield was observed for any technology/hybrid. In these studies, corn earworm larvae did not cause enough damage to impact yield. Additionally, no consistent relationship between corn earworm damage and aflatoxin contamination was observed. Based on these data, the economic value of pyramided Bt corn traits to corn producers, in the southern United States, appears to be from management of other lepidopteran insect pests including European and southwestern corn borer.

Diverse Bacteria Inhabit Living Hyphae of Phylogenetically Diverse Fungal Endophytes▿ †

PubMed Central

Hoffman, Michele T.; Arnold, A. Elizabeth

2010-01-01

Both the establishment and outcomes of plant-fungus symbioses can be influenced by abiotic factors, the interplay of fungal and plant genotypes, and additional microbes associated with fungal mycelia. Recently bacterial endosymbionts were documented in soilborne Glomeromycota and Mucoromycotina and in at least one species each of mycorrhizal Basidiomycota and Ascomycota. Here we show for the first time that phylogenetically diverse endohyphal bacteria occur in living hyphae of diverse foliar endophytes, including representatives of four classes of Ascomycota. We examined 414 isolates of endophytic fungi, isolated from photosynthetic tissues of six species of cupressaceous trees in five biogeographic provinces, for endohyphal bacteria using microscopy and molecular techniques. Viable bacteria were observed within living hyphae of endophytic Pezizomycetes, Dothideomycetes, Eurotiomycetes, and Sordariomycetes from all tree species and biotic regions surveyed. A focus on 29 fungus/bacterium associations revealed that bacterial and fungal phylogenies were incongruent with each other and with taxonomic relationships of host plants. Overall, eight families and 15 distinct genotypes of endohyphal bacteria were recovered; most were members of the Proteobacteria, but a small number of Bacillaceae also were found, including one that appears to occur as an endophyte of plants. Frequent loss of bacteria following subculturing suggests a facultative association. Our study recovered distinct lineages of endohyphal bacteria relative to previous studies, is the first to document their occurrence in foliar endophytes representing four of the most species-rich classes of fungi, and highlights for the first time their diversity and phylogenetic relationships with regard both to the endophytes they inhabit and the plants in which these endophyte-bacterium symbiota occur. PMID:20435775

Cold active hydrolytic enzymes production by psychrotrophic Bacilli isolated from three sub-glacial lakes of NW Indian Himalayas.

PubMed

Yadav, Ajar Nath; Sachan, Shashwati Ghosh; Verma, Priyanka; Kaushik, Rajeev; Saxena, Anil Kumar

2016-03-01

The diversity of culturable, cold-active enzymes producing Bacilli was investigated from three sub-glacial lakes of north western Indian Himalayas. Amplified ribosomal DNA restriction analysis (ARDRA) using three restriction enzymes Alu I, Msp I, and Hae III led to the clustering of 136 Bacilli into 26, 23, and 22 clusters at 75% similarity index from Chandratal Lake, Dashair Lake, and Pangong Lake, respectively. Phylogenetic analysis based on 16S rRNA gene sequencing led to the identification of 35 Bacilli that could be grouped in seven families viz.: Bacillaceae (48%), Staphylococcaceae (14%), Bacillales incertae sedis (13%), Planococcaceae (12%), Paenibacillaceae (9%), Sporolactobacillaceae (3%), and Carnobacteriaceae (1%), which included twelve different genera Bacillus, Desemzia, Exiguobacterium, Jeotgalicoccus, Lysinibacillus, Paenibacillus, Planococcus, Pontibacillus, Sinobaca, Sporosarcina, Staphylococcus, and Virgibacillus. Based on their optimal temperature for growth, 35 Bacilli were grouped as psychrophilic (11 strains), psychrotrophic (17 strains), or psychrotolerant (7 strains), respectively. The representative isolates from each cluster were screened for cold-active enzyme activities. Amylase, β-glucosidase, pectinase, and protease activities at 4 °C were detected in more than 80% of the strains while approximately 40, 31, 23, 14, 11, and 9% of strains possessed cellulase, xylanase, β-galactosidase, laccase, chitinase, and lipase activity, respectively. Among 35 Bacilli, Bacillus amyloliquefaciens, Bacillus marisflavi, Exiguobacterium indicum, Paenibacillus terrae, Pontibacillus sp., Sporosarcina globispora, and Sporosarcina psychrophila were efficient producers of different cold-active enzymes. These cold-adapted Bacilli could play an important role in industrial and agricultural processes. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Isolation and characterization of microorganisms and volatiles associated with Moroccan saffron during different processing treatments.

PubMed

Fancello, Francesco; Petretto, Giacomo; Sanna, Maria Lina; Pintore, Giorgio; Lage, Mounira; Zara, Severino

2018-05-20

Saffron may be spoiled by a variety of microorganisms during cultivation, harvesting, and post harvesting. As saffron can be dried and stored in different ways, this preliminary study explored the natural microbiota present in Moroccan saffron when subjected to different drying techniques. An analysis of the carotenoid-derived volatiles present in the saffron was also carried out. The culturable microbiota of the saffron samples dried using different methods, namely in the shade (also called natural), in the sun, or in the oven, were studied using classical and molecular approaches. The effect of the drying methods on head-space chemical volatiles was also determined. Eighty-two isolates grown in the different culture media were chosen from the colonies, and genotype analysis grouped the microorganisms into 58 clusters, revealing a wide diversity. Out of the 82 isolates, 75 belonged to the Bacillaceae family. The other isolates were distributed within the Dietziaceae, Paenibacillaceae and Carnobacteriaceae families. The dominant species was Bacillus simplex, which was detected in all samples, regardless of the drying method used. Lysinibacillus macroides was dominant in the sun-dried saffron. No pathogens were isolated, but an isolate belonging to Dietzia maris, a potential human pathogenic species, was detected. The biodiversity indexes were linked to the drying method and generally decreased as the intensity of the treatment increased. The results of this preliminary work show that the different drying methods strongly influenced the microbiota and affect the saffron volatile profile. Further analysis will be needed to determine possible effects of selected microbiota on saffron volatiles. Copyright © 2018 Elsevier B.V. All rights reserved.

Multiple genome alignment for identifying the core structure among moderately related microbial genomes.

PubMed

Uchiyama, Ikuo

2008-10-31

Identifying the set of intrinsically conserved genes, or the genomic core, among related genomes is crucial for understanding prokaryotic genomes where horizontal gene transfers are common. Although core genome identification appears to be obvious among very closely related genomes, it becomes more difficult when more distantly related genomes are compared. Here, we consider the core structure as a set of sufficiently long segments in which gene orders are conserved so that they are likely to have been inherited mainly through vertical transfer, and developed a method for identifying the core structure by finding the order of pre-identified orthologous groups (OGs) that maximally retains the conserved gene orders. The method was applied to genome comparisons of two well-characterized families, Bacillaceae and Enterobacteriaceae, and identified their core structures comprising 1438 and 2125 OGs, respectively. The core sets contained most of the essential genes and their related genes, which were primarily included in the intersection of the two core sets comprising around 700 OGs. The definition of the genomic core based on gene order conservation was demonstrated to be more robust than the simpler approach based only on gene conservation. We also investigated the core structures in terms of G+C content homogeneity and phylogenetic congruence, and found that the core genes primarily exhibited the expected characteristic, i.e., being indigenous and sharing the same history, more than the non-core genes. The results demonstrate that our strategy of genome alignment based on gene order conservation can provide an effective approach to identify the genomic core among moderately related microbial genomes.

Variability, stability, and resilience of fecal microbiota in dairy cows fed whole crop corn silage.

PubMed

Tang, Minh Thuy; Han, Hongyan; Yu, Zhu; Tsuruta, Takeshi; Nishino, Naoki

2017-08-01

The microbiota of whole crop corn silage and feces of silage-fed dairy cows were examined. A total of 18 dairy cow feces were collected from six farms in Japan and China, and high-throughput Illumina sequencing of the V4 hypervariable region of 16S rRNA genes was performed. Lactobacillaceae were dominant in all silages, followed by Acetobacteraceae, Bacillaceae, and Enterobacteriaceae. In feces, the predominant families were Ruminococcaceae, Bacteroidaceae, Clostridiaceae, Lachnospiraceae, Rikenellaceae, and Paraprevotellaceae. Therefore, Lactobacillaceae of corn silage appeared to be eliminated in the gastrointestinal tract. Although fecal microbiota composition was similar in most samples, relative abundances of several families, such as Ruminococcaceae, Christensenellaceae, Turicibacteraceae, and Succinivibrionaceae, varied between farms and countries. In addition to the geographical location, differences in feeding management between total mixed ration feeding and separate feeding appeared to be involved in the variations. Moreover, a cow-to-cow variation for concentrate-associated families was demonstrated at the same farm; two cows showed high abundance of Succinivibrionaceae and Prevotellaceae, whereas another had a high abundance of Porphyromonadaceae. There was a negative correlation between forage-associated Ruminococcaceae and concentrate-associated Succinivibrionaceae and Prevotellaceae in 18 feces samples. Succinivibrionaceae, Prevotellaceae, p-2534-18B5, and Spirochaetaceae were regarded as highly variable taxa in this study. These findings help to improve our understanding of variation and similarity of the fecal microbiota of dairy cows with regard to individuals, farms, and countries. Microbiota of naturally fermented corn silage had no influence on the fecal microbiota of dairy cows.

pH and Organic Carbon Dose Rates Control Microbially Driven Bioremediation Efficacy in Alkaline Bauxite Residue.

PubMed

Santini, Talitha C; Malcolm, Laura I; Tyson, Gene W; Warren, Lesley A

2016-10-18

Bioremediation of alkaline tailings, based on fermentative microbial metabolisms, is a novel strategy for achieving rapid pH neutralization and thus improving environmental outcomes associated with mining and refining activities. Laboratory-scale bioreactors containing bauxite residue (an alkaline, saline tailings material generated as a byproduct of alumina refining), to which a diverse microbial inoculum was added, were used in this study to identify key factors (pH, salinity, organic carbon supply) controlling the rates and extent of microbially driven pH neutralization (bioremediation) in alkaline tailings. Initial tailings pH and organic carbon dose rates both significantly affected bioremediation extent and efficiency with lower minimum pHs and higher extents of pH neutralization occurring under low initial pH or high organic carbon conditions. Rates of pH neutralization (up to 0.13 mM H + produced per day with pH decreasing from 9.5 to ≤6.5 in three days) were significantly higher in low initial pH treatments. Representatives of the Bacillaceae and Enterobacteriaceae, which contain many known facultative anaerobes and fermenters, were identified as key contributors to 2,3-butanediol and/or mixed acid fermentation as the major mechanism(s) of pH neutralization. Initial pH and salinity significantly influenced microbial community successional trajectories, and microbial community structure was significantly related to markers of fermentation activity. This study provides the first experimental demonstration of bioremediation in bauxite residue, identifying pH and organic carbon dose rates as key controls on bioremediation efficacy, and will enable future development of bioreactor technologies at full field scale.

The microbiota of eight species of dehydrated edible seaweeds from North West Spain.

PubMed

Del Olmo, Ana; Picon, Antonia; Nuñez, Manuel

2018-04-01

The microbiota of eight species (Chondrus crispus, Himanthalia elongata, Laminaria ochroleuca, Palmaria palmata, Porphyra umbilicalis, Saccharina latissima, Ulva lactuca and Undaria pinnatifida) of edible seaweeds collected in North West Spain, marketed as dehydrated product, was quantitatively determined on nine solid media. Representative colonies were selected from solid culture media. The isolated microorganisms were identified by means of morphological characteristics, 16S rDNA sequencing and biochemical tests. U. pinnatifida was the seaweed species showing the most abundant microbial population, with counts on Marine agar up to 7.7 log cfu/g in individual samples and 5.0 log cfu/g as the mean value, and counts of coliforms up to 4.6 log cfu/g in individual samples and 2.4 log cfu/g as the mean value. The 225 identified bacterial isolates belonged to 11 families, 27 genera and 56 species. Bacillaceae was the family accounting for the highest number of isolates (111) followed by Enterobacteriaceae (60), Bacillales Family XII Incertae Sedis (20), Planococcaceae (11), Moraxellaceae (7), Paenibacillaceae (5) and Pseudomonadaceae (5). Bacterial species showing the highest occurrence in dehydrated seaweeds were Bacillus megaterium, B. licheniformis, Pantoea sp. and termoresistant Pantoea sp. Four of the Bacillus species isolated from dehydrated seaweeds (B. cereus, B. licheniformis, B. pumilus and B. subtilis) are among those containing strains considered to be foodborne pathogens and nine of the isolated non-Bacillales bacterial species have been reported to contain human opportunistic pathogenic strains. Copyright © 2017 Elsevier Ltd. All rights reserved.

Isolation and Characterization of Bacteria Capable of Tolerating the Extreme Conditions of Clean Room Environments▿

PubMed Central

La Duc, Myron T.; Dekas, Anne; Osman, Shariff; Moissl, Christine; Newcombe, David; Venkateswaran, Kasthuri

2007-01-01

In assessing the bacterial populations present in spacecraft assembly, spacecraft test, and launch preparation facilities, extremophilic bacteria (requiring severe conditions for growth) and extremotolerant bacteria (tolerant to extreme conditions) were isolated. Several cultivation approaches were employed to select for and identify bacteria that not only survive the nutrient-limiting conditions of clean room environments but can also withstand even more inhospitable environmental stresses. Due to their proximity to spacefaring objects, these bacteria pose a considerable risk for forward contamination of extraterrestrial sites. Samples collected from four geographically distinct National Aeronautics and Space Administration clean rooms were challenged with UV-C irradiation, 5% hydrogen peroxide, heat shock, pH extremes (pH 3.0 and 11.0), temperature extremes (4°C to 65°C), and hypersalinity (25% NaCl) prior to and/or during cultivation as a means of selecting for extremotolerant bacteria. Culture-independent approaches were employed to measure viable microbial (ATP-based) and total bacterial (quantitative PCR-based) burdens. Intracellular ATP concentrations suggested a viable microbial presence ranging from below detection limits to 106 cells/m2. However, only 0.1 to 55% of these viable cells were able to grow on defined culture medium. Isolated members of the Bacillaceae family were more physiologically diverse than those reported in previous studies, including thermophiles (Geobacillus), obligate anaerobes (Paenibacillus), and halotolerant, alkalophilic species (Oceanobacillus and Exiguobacterium). Non-spore-forming microbes (α- and β-proteobacteria and actinobacteria) exhibiting tolerance to the selected stresses were also encountered. The multiassay cultivation approach employed herein enhances the current understanding of the physiological diversity of bacteria housed in these clean rooms and leads us to ponder the origin and means of translocation of thermophiles, anaerobes, and halotolerant alkalophiles into these environments. PMID:17308177

Bacterial Symbionts in Lepidoptera: Their Diversity, Transmission, and Impact on the Host

PubMed Central

Paniagua Voirol, Luis R.; Frago, Enric; Kaltenpoth, Martin; Hilker, Monika; Fatouros, Nina E.

2018-01-01

The insect’s microbiota is well acknowledged as a “hidden” player influencing essential insect traits. The gut microbiome of butterflies and moths (Lepidoptera) has been shown to be highly variable between and within species, resulting in a controversy on the functional relevance of gut microbes in this insect order. Here, we aim to (i) review current knowledge on the composition of gut microbial communities across Lepidoptera and (ii) elucidate the drivers of the variability in the lepidopteran gut microbiome and provide an overview on (iii) routes of transfer and (iv) the putative functions of microbes in Lepidoptera. To find out whether Lepidopterans possess a core gut microbiome, we compared studies of the microbiome from 30 lepidopteran species. Gut bacteria of the Enterobacteriaceae, Bacillaceae, and Pseudomonadaceae families were the most widespread across species, with Pseudomonas, Bacillus, Staphylococcus, Enterobacter, and Enterococcus being the most common genera. Several studies indicate that habitat, food plant, and age of the host insect can greatly impact the gut microbiome, which contributes to digestion, detoxification, or defense against natural enemies. We mainly focus on the gut microbiome, but we also include some examples of intracellular endosymbionts. These symbionts are present across a broad range of insect taxa and are known to exert different effects on their host, mostly including nutrition and reproductive manipulation. Only two intracellular bacteria genera (Wolbachia and Spiroplasma) have been reported to colonize reproductive tissues of Lepidoptera, affecting their host’s reproduction. We explore routes of transmission of both gut microbiota and intracellular symbionts and have found that these microbes may be horizontally transmitted through the host plant, but also vertically via the egg stage. More detailed knowledge about the functions and plasticity of the microbiome in Lepidoptera may provide novel leads for the control of lepidopteran pest species. PMID:29636736

Pelagirhabdus alkalitolerans gen. nov., sp. nov., an alkali-tolerant and thermotolerant bacterium isolated from beach sediment, and reclassification of Amphibacillus fermentum as Pelagirhabdus fermentum comb. nov.

PubMed

Sultanpuram, Vishnuvardhan Reddy; Mothe, Thirumala; Chintalapati, Sasikala; Chintalapati, Venkata Ramana

2016-01-01

A novel bacterial strain, designated S5T, was isolated from Pingaleshwar beach, in India. Cells were Gram-stain-positive, rod-shaped, non-motile and non-endospore-forming. Based on 16S rRNA gene sequence analysis, the strain was identified as belonging to the class Firmibacteria and was related most closely to Amphibacillus fermentum DSM 13869T (97.6 % sequence similarity). However, it shared only 93.1 % 16S rRNA gene sequence similarity with Amphibacillus xylanus NBRC 15112T, the type species of the genus, indicating that strain S5T might not be a member of the genus Amphibacillus. The DNA-DNA relatedness between strain S5T and Amphibacillus fermentum DSM 13869T was 39 %. The cell-wall peptidoglycan contained meso-diaminopimelic acid. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol and two phospholipids. Isoprenoid quinones were absent from strain S5T. Fatty acid analysis revealed that anteiso-C15 : 0, C16 : 0 and iso-C15 : 0 were the predominant fatty acids present. The results of phylogenetic, chemotaxonomic and biochemical tests allowed the clear differentiation of strain S5T, which is considered to represent a novel species of a new genus in the family Bacillaceae, for which the name Pelagirhabdus alkalitolerans gen. nov., sp. nov. is proposed. The type strain of Pelagirhabdus alkalitolerans is S5T ( = KCTC 33632T = CGMCC 1.15177T). Based on the present study, it is also suggested to transfer Amphibacillus fermentum to this new genus, as Pelagirhabdus fermentum comb. nov. The type strain of Pelagirhabdus fermentum is Z-7984T = (DSM 13869T = UNIQEM 210T).

Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes

PubMed Central

Galperin, Michael Y; Mekhedov, Sergei L; Puigbo, Pere; Smirnov, Sergey; Wolf, Yuri I; Rigden, Daniel J

2012-01-01

Three classes of low-G+C Gram-positive bacteria (Firmicutes), Bacilli, Clostridia and Negativicutes, include numerous members that are capable of producing heat-resistant endospores. Spore-forming firmicutes include many environmentally important organisms, such as insect pathogens and cellulose-degrading industrial strains, as well as human pathogens responsible for such diseases as anthrax, botulism, gas gangrene and tetanus. In the best-studied model organism Bacillus subtilis, sporulation involves over 500 genes, many of which are conserved among other bacilli and clostridia. This work aimed to define the genomic requirements for sporulation through an analysis of the presence of sporulation genes in various firmicutes, including those with smaller genomes than B. subtilis. Cultivable spore-formers were found to have genomes larger than 2300 kb and encompass over 2150 protein-coding genes of which 60 are orthologues of genes that are apparently essential for sporulation in B. subtilis. Clostridial spore-formers lack, among others, spoIIB, sda, spoVID and safA genes and have non-orthologous displacements of spoIIQ and spoIVFA, suggesting substantial differences between bacilli and clostridia in the engulfment and spore coat formation steps. Many B. subtilis sporulation genes, particularly those encoding small acid-soluble spore proteins and spore coat proteins, were found only in the family Bacillaceae, or even in a subset of Bacillus spp. Phylogenetic profiles of sporulation genes, compiled in this work, confirm the presence of a common sporulation gene core, but also illuminate the diversity of the sporulation processes within various lineages. These profiles should help further experimental studies of uncharacterized widespread sporulation genes, which would ultimately allow delineation of the minimal set(s) of sporulation-specific genes in Bacilli and Clostridia. PMID:22882546

Microbiota dynamics and diversity at different stages of industrial processing of cocoa beans into cocoa powder.

PubMed

Lima, Lídia J R; van der Velpen, Vera; Wolkers-Rooijackers, Judith; Kamphuis, Henri J; Zwietering, Marcel H; Nout, M J Rob

2012-04-01

We sampled a cocoa powder production line to investigate the impact of processing on the microbial community size and diversity at different stages. Classical microbiological methods were combined with 16S rRNA gene PCR-denaturing gradient gel electrophoresis, coupled with clone library construction, to analyze the samples. Aerobic thermoresistant spores (ThrS) (100°C; 10 min) were also isolated and characterized (identity, genetic diversity, and spore heat resistance), in view of their relevance to the quality of downstream heat-treated cocoa-flavored drinks. In the nibs (broken, shelled cocoa beans), average levels of total aerobic microorganisms (TAM) (4.4 to 5.6 log CFU/g) and aerobic total spores (TS) (80°C; 10 min; 4.3 to 5.5 log CFU/g) were significantly reduced (P < 0.05) as a result of alkalizing, while fungi (4.2 to 4.4 log CFU/g) and Enterobacteriaceae (1.7 to 2.8 log CFU/g) were inactivated to levels below the detection limit, remaining undetectable throughout processing. Roasting further decreased the levels of TAM and TS, but they increased slightly during subsequent processing. Molecular characterization of bacterial communities based on enriched cocoa samples revealed a predominance of members of the Bacillaceae, Pseudomonadaceae, and Enterococcaceae. Eleven species of ThrS were found, but Bacillus licheniformis and the Bacillus subtilis complex were prominent and revealed great genetic heterogeneity. We concluded that the microbiota of cocoa powder resulted from microorganisms that could have been initially present in the nibs, as well as microorganisms that originated during processing. B. subtilis complex members, particularly B. subtilis subsp. subtilis, formed the most heat-resistant spores. Their occurrence in cocoa powder needs to be considered to ensure the stability of derived products, such as ultrahigh-temperature-treated chocolate drinks.

Isolation and characterization of bacteria capable of tolerating the extreme conditions of clean room environments.

PubMed

La Duc, Myron T; Dekas, Anne; Osman, Shariff; Moissl, Christine; Newcombe, David; Venkateswaran, Kasthuri

2007-04-01

In assessing the bacterial populations present in spacecraft assembly, spacecraft test, and launch preparation facilities, extremophilic bacteria (requiring severe conditions for growth) and extremotolerant bacteria (tolerant to extreme conditions) were isolated. Several cultivation approaches were employed to select for and identify bacteria that not only survive the nutrient-limiting conditions of clean room environments but can also withstand even more inhospitable environmental stresses. Due to their proximity to spacefaring objects, these bacteria pose a considerable risk for forward contamination of extraterrestrial sites. Samples collected from four geographically distinct National Aeronautics and Space Administration clean rooms were challenged with UV-C irradiation, 5% hydrogen peroxide, heat shock, pH extremes (pH 3.0 and 11.0), temperature extremes (4 degrees C to 65 degrees C), and hypersalinity (25% NaCl) prior to and/or during cultivation as a means of selecting for extremotolerant bacteria. Culture-independent approaches were employed to measure viable microbial (ATP-based) and total bacterial (quantitative PCR-based) burdens. Intracellular ATP concentrations suggested a viable microbial presence ranging from below detection limits to 10(6) cells/m(2). However, only 0.1 to 55% of these viable cells were able to grow on defined culture medium. Isolated members of the Bacillaceae family were more physiologically diverse than those reported in previous studies, including thermophiles (Geobacillus), obligate anaerobes (Paenibacillus), and halotolerant, alkalophilic species (Oceanobacillus and Exiguobacterium). Non-spore-forming microbes (alpha- and beta-proteobacteria and actinobacteria) exhibiting tolerance to the selected stresses were also encountered. The multiassay cultivation approach employed herein enhances the current understanding of the physiological diversity of bacteria housed in these clean rooms and leads us to ponder the origin and means of translocation of thermophiles, anaerobes, and halotolerant alkalophiles into these environments.

Thermophile-fermented compost as a fish feed additive modulates lipid peroxidation and free amino acid contents in the muscle of the carp, Cyprinus carpio.

PubMed

Tanaka, Ryusuke; Miyamoto, Hirokuni; Inoue, Shin-Ichi; Shigeta, Kazuhiro; Kondo, Masakazu; Ito, Toshiyuki; Kodama, Hiroaki; Miyamoto, Hisashi; Matsushita, Teruo

2016-05-01

Recently, a compost fermented with marine animals with thermophilic Bacillaceae in a clean and exclusive process at high temperature was reported as a possible feed additive to improve the healthy balance in sea fish and mammals (i.e., pigs and rodents). Here, the effects of the oral administration of the compost on the muscle and internal organs of carp (Cyprinus carpio) as a freshwater fish model were investigated. The fatty acid composition was different in the muscle of the carp fed with or without the compost extract, but there was little difference in the hepatopancreas. The accumulation of triacylglycerols, cholesterol, lipid peroxide and hydroxyl lipids decreased in the muscle after the oral administration of the compost extract in the carps over 12 weeks, but the accumulation did not always decrease in the hepatopancreas. In contrast, free-radical-scavenging activities and the concentrations of free amino acids in the muscle did not always increase and was dependent on the dose of the compost at 12 weeks. The scavenging activities and part of free amino acid levels in the muscle of the carp were improved at 24 weeks after a high dose of compost exposure, and then the survival rates of the carp were maintained. Thus, the oral administration of thermophile-fermented compost can prevent peroxidation and increase the content of free amino acids in the muscle of the freshwater fish, depending on the dose and term of the administration, and may be associated with the viability of the fish. Copyright © 2015 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Spontaneous cocoa bean fermentation carried out in a novel-design stainless steel tank: influence on the dynamics of microbial populations and physical-chemical properties.

PubMed

de Melo Pereira, Gilberto Vinícius; Magalhães, Karina Teixeira; de Almeida, Euziclei Gonzaga; da Silva Coelho, Irene; Schwan, Rosane Freitas

2013-02-01

Spontaneous cocoa bean fermentations carried out in a novel-design 40-kg-capacity stainless steel tank (SST) was studied in parallel to traditional Brazilian methods of fermentation in wooden boxes (40-kg-capacity wooden boxes (WB1) and 600-kg-capacity wooden boxes (WB2)) using a multiphasic approach that entailed culture-dependent and -independent microbiological analyses of fermenting cocoa bean pulp samples and target metabolite analyses of both cocoa pulp and cotyledons. Both microbiological approaches revealed that the dominant species of major physiological roles were the same for fermentations in SST, relative to boxes. These species consisted of Saccharomyces cerevisiae and Hanseniaspora sp. in the yeast group; Lactobacillus fermentum and L. plantarum in the lactic acid bacteria (LAB) group; Acetobacter tropicalis belonging to the acetic acid bacteria (AAB) group; and Bacillus subtilis in the Bacillaceae family. A greater diversity of bacteria and non-Saccharomyces yeasts was observed in box fermentations. Additionally, a potentially novel AAB belonging to the genus Asaia was isolated during fermentation in WB1. Cluster analysis of the rRNA genes-PCR-DGGE profiles revealed a more complex picture of the box samples, indicating that bacterial and yeast ecology were fermentation-specific processes (wooden boxes vs. SST). The profile of carbohydrate consumption and fermentation products in the pulp and beans showed similar trends during both fermentation processes. However, the yeast-AAB-mediated conversion of carbohydrates into ethanol, and subsequent conversion of ethanol into acetic acid, was achieved with greater efficiency in SST, while temperatures were generally higher during fermentation in wooden boxes. With further refinements, the SST model may be useful in designing novel bioreactors for the optimisation of cocoa fermentation with starter cultures. Copyright © 2012 Elsevier B.V. All rights reserved.

Individual and Combined Effects of Bacillus Thuringiensis and Azadirachtin on Plodia Interpunctella Hübner (Lepidoptera: Pyralidae)

PubMed Central

Nouri-Ganbalani, Gadir; Borzoui, Ehsan; Abdolmaleki, Arman; Abedi, Zahra; George Kamita, Shizuo

2016-01-01

The Indianmeal moth, Plodia interpunctella Hübner (Lepidoptera: Pyralidae), is a major stored product pest that is found throughout the world. In this study, the effect of oral exposure to Bacillus thuringiensis (Berliner) subsp. kurstaki (Bacillales: Bacillaceae) and azadirachtin was evaluated in third instar P. interpunctella under laboratory conditions. The median lethal concentration (LC50) of Bt and azadirachtin on third instars was 490 and 241 μg a.i./ml, respectively. The median lethal time (LT50) of these insecticides was the same (4.5 d following exposure to 750 or 400 μg a.i./ml of Bt or azadirachtin, respectively). When the larvae fed on diet containing LC30 concentrations of both Bt and azadirachtin an additive interaction in terms of mortality was found. A synergistic interaction was found when the larvae fed on diet containing LC50 concentrations of both insecticides. Larvae that fed on insecticide-containing diet (either Bt or azadirachtin at an LC30 concentration, or both insecticides at LC30 or LC50 concentrations) showed lower glycogen and lipid levels, and generally lower protein content in comparison to control larvae. Larvae that fed on diet containing both Bt and azadirachtin showed reduced weight gain and nutritional indices in comparison to control larvae or larvae fed on the diet containing only one of the insecticides. Finally, exposure to both insecticides, either individually or in combination, reduced the level of digestive enzymes found in the midgut. Our findings indicate that both Bt and azadirachtin, either individually or in combination have significant potential for use in controlling of P. interpunctella. PMID:27638953

Individual and Combined Effects of Bacillus Thuringiensis and Azadirachtin on Plodia Interpunctella Hübner (Lepidoptera: Pyralidae).

PubMed

Nouri-Ganbalani, Gadir; Borzoui, Ehsan; Abdolmaleki, Arman; Abedi, Zahra; George Kamita, Shizuo

2016-01-01

The Indianmeal moth, Plodia interpunctella Hübner (Lepidoptera: Pyralidae), is a major stored product pest that is found throughout the world. In this study, the effect of oral exposure to Bacillus thuringiensis (Berliner) subsp. kurstaki (Bacillales: Bacillaceae) and azadirachtin was evaluated in third instar P. interpunctella under laboratory conditions. The median lethal concentration (LC50) of Bt and azadirachtin on third instars was 490 and 241 μg a.i./ml, respectively. The median lethal time (LT50) of these insecticides was the same (4.5 d following exposure to 750 or 400 μg a.i./ml of Bt or azadirachtin, respectively). When the larvae fed on diet containing LC30 concentrations of both Bt and azadirachtin an additive interaction in terms of mortality was found. A synergistic interaction was found when the larvae fed on diet containing LC50 concentrations of both insecticides. Larvae that fed on insecticide-containing diet (either Bt or azadirachtin at an LC30 concentration, or both insecticides at LC30 or LC50 concentrations) showed lower glycogen and lipid levels, and generally lower protein content in comparison to control larvae. Larvae that fed on diet containing both Bt and azadirachtin showed reduced weight gain and nutritional indices in comparison to control larvae or larvae fed on the diet containing only one of the insecticides. Finally, exposure to both insecticides, either individually or in combination, reduced the level of digestive enzymes found in the midgut. Our findings indicate that both Bt and azadirachtin, either individually or in combination have significant potential for use in controlling of P. interpunctella. © The Author 2016. Published by Oxford University Press on behalf of the Entomological Society of America.

Density Dependence and Growth Rate: Evolutionary Effects on Resistance Development to Bt (Bacillus thuringiensis).

PubMed

Martinez, Jeannette C; Caprio, Michael A; Friedenberg, Nicholas A

2018-02-09

It has long been recognized that pest population dynamics can affect the durability of a pesticide, but dose remains the primary component of insect resistance management (IRM). For transgenic pesticidal traits such as Bt (Bacillus thuringiensis Berliner (Bacillales: Bacillaceae)), dose (measured as the mortality of susceptibles caused by a toxin) is a relatively fixed characteristic and often falls below the standard definition of high dose. Hence, it is important to understand how pest population dynamics modify durability and what targets they present for IRM. We used a deterministic model of a generic arthropod pest to examine how timing and strength of density dependence interacted with population growth rate and Bt mortality to affect time to resistance. As in previous studies, durability typically reached a minimum at intermediate doses. However, high population growth rates could eliminate benefits of high dose. The timing of density dependence had a more subtle effect. If density dependence operated simultaneously with Bt mortality, durability was insensitive to its strengths. However, if density dependence was driven by postselection densities, decreasing its strength could increase durability. The strength of density dependence could affect durability of both single traits and pyramids, but its influence depended on the timing of density dependence and size of the refuge. Our findings suggest the utility of a broader definition of high dose, one that incorporates population-dynamic context. That maximum growth rates and timing and strength of interactions causing density dependent mortality can all affect durability, also highlights the need for ecologically integrated approaches to IRM research. © The Author(s) 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Microbiota Dynamics and Diversity at Different Stages of Industrial Processing of Cocoa Beans into Cocoa Powder

PubMed Central

Lima, Lídia J. R.; van der Velpen, Vera; Wolkers-Rooijackers, Judith; Kamphuis, Henri J.; Nout, M. J. Rob

2012-01-01

We sampled a cocoa powder production line to investigate the impact of processing on the microbial community size and diversity at different stages. Classical microbiological methods were combined with 16S rRNA gene PCR-denaturing gradient gel electrophoresis, coupled with clone library construction, to analyze the samples. Aerobic thermoresistant spores (ThrS) (100°C; 10 min) were also isolated and characterized (identity, genetic diversity, and spore heat resistance), in view of their relevance to the quality of downstream heat-treated cocoa-flavored drinks. In the nibs (broken, shelled cocoa beans), average levels of total aerobic microorganisms (TAM) (4.4 to 5.6 log CFU/g) and aerobic total spores (TS) (80°C; 10 min; 4.3 to 5.5 log CFU/g) were significantly reduced (P < 0.05) as a result of alkalizing, while fungi (4.2 to 4.4 log CFU/g) and Enterobacteriaceae (1.7 to 2.8 log CFU/g) were inactivated to levels below the detection limit, remaining undetectable throughout processing. Roasting further decreased the levels of TAM and TS, but they increased slightly during subsequent processing. Molecular characterization of bacterial communities based on enriched cocoa samples revealed a predominance of members of the Bacillaceae, Pseudomonadaceae, and Enterococcaceae. Eleven species of ThrS were found, but Bacillus licheniformis and the Bacillus subtilis complex were prominent and revealed great genetic heterogeneity. We concluded that the microbiota of cocoa powder resulted from microorganisms that could have been initially present in the nibs, as well as microorganisms that originated during processing. B. subtilis complex members, particularly B. subtilis subsp. subtilis, formed the most heat-resistant spores. Their occurrence in cocoa powder needs to be considered to ensure the stability of derived products, such as ultrahigh-temperature-treated chocolate drinks. PMID:22327588

Molecular diversity and multifarious plant growth promoting attributes of Bacilli associated with wheat (Triticum aestivum L.) rhizosphere from six diverse agro-ecological zones of India.

PubMed

Verma, Priyanka; Yadav, Ajar Nath; Khannam, Kazy Sufia; Kumar, Sanjay; Saxena, Anil Kumar; Suman, Archna

2016-01-01

The diversity of culturable Bacilli was investigated in six wheat cultivating agro-ecological zones of India viz: northern hills, north western plains, north eastern plains, central, peninsular, and southern hills. These agro-ecological regions are based on the climatic conditions such as pH, salinity, drought, and temperature. A total of 395 Bacilli were isolated by heat enrichment and different growth media. Amplified ribosomal DNA restriction analysis using three restriction enzymes AluI, MspI, and HaeIII led to the clustering of these isolates into 19-27 clusters in the different zones at >70% similarity index, adding up to 137 groups. Phylogenetic analysis based on 16S rRNA gene sequencing led to the identification of 55 distinct Bacilli that could be grouped in five families, Bacillaceae (68%), Paenibacillaceae (15%), Planococcaceae (8%), Staphylococcaceae (7%), and Bacillales incertae sedis (2%), which included eight genera namely Bacillus, Exiguobacterium, Lysinibacillus, Paenibacillus, Planococcus, Planomicrobium, Sporosarcina, and Staphylococcus. All 395 isolated Bacilli were screened for their plant growth promoting attributes, which included direct-plant growth promoting (solubilization of phosphorus, potassium, and zinc; production of phytohormones; 1-aminocyclopropane-1-carboxylate deaminase activity and nitrogen fixation), and indirect-plant growth promotion (antagonistic, production of lytic enzymes, siderophore, hydrogen cyanide, and ammonia). To our knowledge, this is the first report for the presence of Bacillus endophyticus, Paenibacillus xylanexedens, Planococcus citreus, Planomicrobium okeanokoites, Sporosarcina sp., and Staphylococcus succinus in wheat rhizosphere and exhibit multifunctional PGP attributes. These niche-specific and multifarious PGP Bacilli may serve as inoculants for crops growing in respective climatic conditions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Green Microbial Fuel Cell-Based Biosensor for In Situ Chromium (VI) Measurement in Electroplating Wastewater.

PubMed

Wu, Li-Chun; Tsai, Teh-Hua; Liu, Man-Hai; Kuo, Jui-Ling; Chang, Yung-Chu; Chung, Ying-Chien

2017-10-27

The extensive use of Cr(VI) in many industries and the disposal of Cr(VI)-containing wastes have resulted in Cr(VI)-induced environmental contamination. Cr(VI) compounds are associated with increased cancer risks; hence, the detection of toxic Cr(VI) compounds is crucial. Various methods have been developed for Cr(VI) measurement, but they are often conducted offsite and cannot provide real-time toxicity monitoring. A microbial fuel cell (MFC) is an eco-friendly and self-sustaining device that has great potential as a biosensor for in situ Cr(VI) measurement, especially for wastewater generated from different electroplating units. In this study, Exiguobacterium aestuarii YC211, a facultatively anaerobic, Cr(VI)-reducing, salt-tolerant, and exoelectrogenic bacterium, was isolated and inoculated into an MFC to evaluate its feasibility as a Cr(VI) biosensor. The Cr(VI) removal efficiency of E. aestuarii YC211 was not affected by the surrounding environment (pH 5-9, 20-35 °C, coexisting ions, and salinity of 0-15 g/L). The maximum power density of the MFC biosensor was 98.3 ± 1.5 mW/m² at 1500 Ω. A good linear relationship ( r ² = 0.997) was observed between the Cr(VI) concentration (2.5-60 mg/L) and the voltage output. The developed MFC biosensor is a simple device that can accurately measure Cr(VI) concentrations in the actual electroplating wastewater that is generated from different electroplating units within 30 min with low deviations (-6.1% to 2.2%). After treating the actual electroplating wastewater with the MFC, the predominant family in the biofilm was found to be Bacillaceae (95.3%) and was further identified as the originally inoculated E. aestuarii YC211 by next generation sequencing (NGS). Thus, the MFC biosensor can measure Cr(VI) concentrations in situ in the effluents from different electroplating units, and it can potentially help in preventing the violation of effluent regulations.

A Green Microbial Fuel Cell-Based Biosensor for In Situ Chromium (VI) Measurement in Electroplating Wastewater

PubMed Central

Wu, Li-Chun; Tsai, Teh-Hua; Liu, Man-Hai; Kuo, Jui-Ling; Chang, Yung-Chu

2017-01-01

The extensive use of Cr(VI) in many industries and the disposal of Cr(VI)-containing wastes have resulted in Cr(VI)-induced environmental contamination. Cr(VI) compounds are associated with increased cancer risks; hence, the detection of toxic Cr(VI) compounds is crucial. Various methods have been developed for Cr(VI) measurement, but they are often conducted offsite and cannot provide real-time toxicity monitoring. A microbial fuel cell (MFC) is an eco-friendly and self-sustaining device that has great potential as a biosensor for in situ Cr(VI) measurement, especially for wastewater generated from different electroplating units. In this study, Exiguobacterium aestuarii YC211, a facultatively anaerobic, Cr(VI)-reducing, salt-tolerant, and exoelectrogenic bacterium, was isolated and inoculated into an MFC to evaluate its feasibility as a Cr(VI) biosensor. The Cr(VI) removal efficiency of E. aestuarii YC211 was not affected by the surrounding environment (pH 5–9, 20–35 °C, coexisting ions, and salinity of 0–15 g/L). The maximum power density of the MFC biosensor was 98.3 ± 1.5 mW/m2 at 1500 Ω. A good linear relationship (r2 = 0.997) was observed between the Cr(VI) concentration (2.5–60 mg/L) and the voltage output. The developed MFC biosensor is a simple device that can accurately measure Cr(VI) concentrations in the actual electroplating wastewater that is generated from different electroplating units within 30 min with low deviations (−6.1% to 2.2%). After treating the actual electroplating wastewater with the MFC, the predominant family in the biofilm was found to be Bacillaceae (95.3%) and was further identified as the originally inoculated E. aestuarii YC211 by next generation sequencing (NGS). Thus, the MFC biosensor can measure Cr(VI) concentrations in situ in the effluents from different electroplating units, and it can potentially help in preventing the violation of effluent regulations. PMID:29076985

Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes.

PubMed

Galperin, Michael Y; Mekhedov, Sergei L; Puigbo, Pere; Smirnov, Sergey; Wolf, Yuri I; Rigden, Daniel J

2012-11-01

Three classes of low-G+C Gram-positive bacteria (Firmicutes), Bacilli, Clostridia and Negativicutes, include numerous members that are capable of producing heat-resistant endospores. Spore-forming firmicutes include many environmentally important organisms, such as insect pathogens and cellulose-degrading industrial strains, as well as human pathogens responsible for such diseases as anthrax, botulism, gas gangrene and tetanus. In the best-studied model organism Bacillus subtilis, sporulation involves over 500 genes, many of which are conserved among other bacilli and clostridia. This work aimed to define the genomic requirements for sporulation through an analysis of the presence of sporulation genes in various firmicutes, including those with smaller genomes than B. subtilis. Cultivable spore-formers were found to have genomes larger than 2300 kb and encompass over 2150 protein-coding genes of which 60 are orthologues of genes that are apparently essential for sporulation in B. subtilis. Clostridial spore-formers lack, among others, spoIIB, sda, spoVID and safA genes and have non-orthologous displacements of spoIIQ and spoIVFA, suggesting substantial differences between bacilli and clostridia in the engulfment and spore coat formation steps. Many B. subtilis sporulation genes, particularly those encoding small acid-soluble spore proteins and spore coat proteins, were found only in the family Bacillaceae, or even in a subset of Bacillus spp. Phylogenetic profiles of sporulation genes, compiled in this work, confirm the presence of a common sporulation gene core, but also illuminate the diversity of the sporulation processes within various lineages. These profiles should help further experimental studies of uncharacterized widespread sporulation genes, which would ultimately allow delineation of the minimal set(s) of sporulation-specific genes in Bacilli and Clostridia. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.

Effect of the pollution level on the functional bacterial groups aiming at degrading bisphenol A and nonylphenol in natural biofilms of an urban river.

PubMed

Cai, Wei; Li, Yi; Wang, Peifang; Niu, Lihua; Zhang, Wenlong; Wang, Chao

2016-08-01

Bisphenol A (BPA) and 4-nonylphenol (NP) are ubiquitous pollutants with estrogenic activity in aquatic environment and have attracted global concern due to their disruption of endocrine systems. This study investigated the spatial distribution characteristics of the bacterial groups involved in the degradation of BPA and NP within biofilms in an urban river using terminal restriction fragment length polymorphism based on 16S rRNA gene sequences. The effects of the pollution level and water parameters on these groups were also assessed. Hierarchical cluster analysis grouped the sampling sites into three clusters reflecting their varying nutrient pollution levels of relatively slight pollution (SP), moderate pollution (MP), and high pollution (HP) based on water quality data and Environmental Quality Standard for Surface Water of China (GB3838-2002). The BPA and NP concentration in river water ranged from 0.8 to 77.5 and 10.2 to 162.9 ng L(-1), respectively. Comamonadaceae, Pseudomonadaceae, Alcaligenaceae, Bacillaceae, Sphingomonadacea, Burkholderiaceae, and Rhizobiaceae were the dominant bacterial taxa involved in BPA and NP degradation, comprising an average of 9.8, 8.1, 7.6, 6.7, 6.2, 4.1, and 2.8 % of total sequences, respectively. The total abundance of these groups showed a slight upward trend and subsequently rapidly decreased with increasing pollution levels. The average proportion of Comamonadaceae in MP river sections was almost 1.5-2 times than that in SP or HP one. The distribution of functional groups was found related to environmental variables, especially pH, conductivity, ammonium nitrogen (NH3-N), and BPA. The abundance of Comamonadaceae and Rhizobiaceae was both closely related to higher values of pH and conductivity as well as lower concentrations of NP and BPA. Alcaligenaceae and Pseudomonadaceae were associated with higher concentrations of TP and CODMn and inversely correlated with DO concentration. This study might provide effective data on bacterial group changes in polluted urban rivers.

Rapid regrowth and detection of microbial contaminants in equine fecal microbiome samples

PubMed Central

Beckers, Kalie F.; Childers, Gary W.

2017-01-01

Advances have been made to standardize 16S rRNA gene amplicon based studies for inter-study comparisons, yet there are many opportunities for systematic error that may render these comparisons improper and misleading. The fecal microbiome of horses has been examined previously, however, no universal horse fecal collection method and sample processing procedure has been established. This study was initialized in large part to ensure that samples collected by different individuals from different geographical areas (i.e., crowdsourced) were not contaminated due to less than optimal sampling or holding conditions. In this study, we examined the effect of sampling the surface of fecal pellets compared to homogenized fecal pellets, and also the effect of time of sampling after defecation on ‘bloom’ taxa (bloom taxa refers to microbial taxa that can grow rapidly in horse feces post-defecation) using v4 16S rRNA amplicon libraries. A total of 1,440,171 sequences were recovered from 65 horse fecal samples yielding a total of 3,422 OTUs at 97% similarity. Sampling from either surface or homogenized feces had no effect on diversity and little effect on microbial composition. Sampling at various time points (0, 2, 4, 6, 12 h) had a significant effect on both diversity and community composition of fecal samples. Alpha diversity (Shannon index) initially increased with time as regrowth taxa were detected in the amplicon libraries, but by 12 h the diversity sharply decreased as the community composition became dominated by a few bloom families, including Bacillaceae, Planococcaeae, and Enterococcaceae, and other families to a lesser extent. The results show that immediate sampling of horse feces must be done in order to ensure accurate representation of horse fecal samples. Also, several of the bloom taxa found in this study are known to occur in human and cattle feces post defecation. The dominance of these taxa in feces shortly after defecation suggests that the feces is an important habitat for these organisms, and horse fecal samples that were improperly stored can be identified by presence of bloom taxa. PMID:29091944

Microbial succession in an inflated lunar/Mars analog habitat during a 30-day human occupation.

PubMed

Mayer, Teresa; Blachowicz, Adriana; Probst, Alexander J; Vaishampayan, Parag; Checinska, Aleksandra; Swarmer, Tiffany; de Leon, Pablo; Venkateswaran, Kasthuri

2016-06-02

For potential future human missions to the Moon or Mars and sustained presence in the International Space Station, a safe enclosed habitat environment for astronauts is required. Potential microbial contamination of closed habitats presents a risk for crewmembers due to reduced human immune response during long-term confinement. To make future habitat designs safer for crewmembers, lessons learned from characterizing analogous habitats is very critical. One of the key issues is that how human presence influences the accumulation of microorganisms in the closed habitat. Molecular technologies, along with traditional microbiological methods, were utilized to catalog microbial succession during a 30-day human occupation of a simulated inflatable lunar/Mars habitat. Surface samples were collected at different time points to capture the complete spectrum of viable and potential opportunistic pathogenic bacterial population. Traditional cultivation, propidium monoazide (PMA)-quantitative polymerase chain reaction (qPCR), and adenosine triphosphate (ATP) assays were employed to estimate the cultivable, viable, and metabolically active microbial population, respectively. Next-generation sequencing was used to elucidate the microbial dynamics and community profiles at different locations of the habitat during varying time points. Statistical analyses confirm that occupation time has a strong influence on bacterial community profiles. The Day 0 samples (before human occupation) have a very different microbial diversity compared to the later three time points. Members of Proteobacteria (esp. Oxalobacteraceae and Caulobacteraceae) and Firmicutes (esp. Bacillaceae) were most abundant before human occupation (Day 0), while other members of Firmicutes (Clostridiales) and Actinobacteria (esp. Corynebacteriaceae) were abundant during the 30-day occupation. Treatment of samples with PMA (a DNA-intercalating dye for selective detection of viable microbial population) had a significant effect on the microbial diversity compared to non-PMA-treated samples. Statistical analyses revealed a significant difference in community structure of samples over time, particularly of the bacteriomes existing before human occupation of the habitat (Day 0 sampling) and after occupation (Day 13, Day 20, and Day 30 samplings). Actinobacteria (mainly Corynebacteriaceae) and Firmicutes (mainly Clostridiales Incertae Sedis XI and Staphylococcaceae) were shown to increase over the occupation time period. The results of this study revealed a strong relationship between human presence and succession of microbial diversity in a closed habitat. Consequently, it is necessary to develop methods and tools for effective maintenance of a closed system to enable safe human habitation in enclosed environments on Earth and beyond.

Medicago truncatula Gaertn. as a model for understanding the mechanism of growth promotion by bacteria from rhizosphere and nodules of alfalfa.

PubMed

Kisiel, Anna; Kępczyńska, Ewa

2016-05-01

The present study showed all the 16 strains isolated and identified from the alfalfa rhizosphere and nodules, and registered in GenBank, to be good candidates for targeted use in studies addressing the rather weak known mechanism of plant growth promotion, including that of Medicago truncatula, a molecular crop model. Based on physiological, biochemical and molecular analysis, the 16 isolates obtained were ascribed to the following five families: Bacillaceae, Rhizobiaceae, Xantomonadaceae, Enterobacteriaceae and Pseudomonadaceae, within which 9 genera and 16 species were identified. All these bacteria were found to significantly enhance fresh and dry weight of root, shoots and whole 5-week-old seedlings. The bacteria were capable of the in vitro use of tryptophan to produce indolic compounds at various concentrations. The ability of almost all the strains to enhance growth of seedlings and individual roots was positively correlated with the production of the indolic compounds (r = 0.69; P = 0.0001), but not with the 1-aminocyclopropane-1-carboxylate deaminase (ACCD) activity (no correlation). For some strains, it was difficult to conclude whether the growth promotion was related to the production of indolic compounds or to the ACCD activity. It is likely that promotion of M. truncatula root development involves also root interaction with pseudomonads, known to produce 2,4-diacetylphloroglucinol (DAPG), a secondary metabolite reported to alter the root architecture by interacting with an auxin-dependent signaling pathway. Inoculation of seedlings with Pseudomonas brassicacearum KK 5, a bacterium known for its lowest ability to produce indolic compounds, the highest ACCD activity and the presence of the phlD gene responsible for DAPG precursor synthesis, resulted in a substantial promotion of root development. Inoculation with the strain increased the endogenous IAA level in M. truncatula leaves after inoculation of 5-week-old seedlings. Three other strains examined in this study also increased the IAA level in the leaves upon inoculation. Moreover, several other factors such as mobilization of phosphorus and zinc to make them available to plants, iron sequestration by siderophore production and the ability to ammonia production also contributed substantially to the phytostimulatory biofertilizing potential of isolated strains. There is, thus, evidence that Medicago truncatula growth promotion by rhizobacteria involves more than one mechanism.

Aquibacillus halophilus gen. nov., sp. nov., a moderately halophilic bacterium from a hypersaline lake, and reclassification of Virgibacillus koreensis as Aquibacillus koreensis comb. nov. and Virgibacillus albus as Aquibacillus albus comb. nov.

PubMed

Amoozegar, Mohammad Ali; Bagheri, Maryam; Didari, Maryam; Mehrshad, Maliheh; Schumann, Peter; Spröer, Cathrin; Sánchez-Porro, Cristina; Ventosa, Antonio

2014-11-01

A novel Gram-stain-positive, moderately halophilic bacterium, designated strain B6B(T), was isolated from the water of an Iranian hypersaline lake, Aran-Bidgol, and characterized taxonomically using a polyphasic approach. Cells of strain B6B(T) were rod-shaped, motile and produced ellipsoidal endospores in terminal positions in non-swollen sporangia. Strain B6B(T) was a strictly aerobic bacterium and catalase- and oxidase-positive. The strain was able to grow at NaCl concentrations of 0.5-20.0% (w/v), with optimum growth occurring at 10.0% (w/v) NaCl. The optimum temperature and pH for growth were 35 °C and pH 7.0. On the basis of 16S rRNA gene sequence analysis, strain B6B(T) was shown to belong to the phylum Firmicutes and its closest phylogenetic similarities were with the species Virgibacillus koreensis BH30097(T) (97.5%), Virgibacillus albus YIM 93624(T) (97.4%), Sediminibacillus halophilus EN8d(T) (96.8%), Sediminibacillus albus NHBX5(T) (96.6%), Virgibacillus carmonensis LMG 20964(T) (96.3%) and Paraliobacillus quinghaiensis YIM-C158(T) (96.0%), respectively. Phylogenetic analysis revealed that strain B6B(T), along with V. koreensis BH30097(T) and V. albus YIM 93624(T), clustered in a separate clade in the family Bacillaceae. The DNA G+C content of the novel isolate was 35.8 mol%. DNA-DNA hybridization experiments revealed low levels of relatedness between strain B6B(T)and V. koreensis BH30097(T) (13%) and V. albus YIM 93624(T) (33%). The major cellular fatty acid of strain B6B(T) was anteiso-C15 : 0 (75.1%) and its polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol, an unknown phospholipid and an unknown glycolipid. The isoprenoid quinones were MK-7 (90%) and MK-6 (3%). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. All of these features support the placement of isolate B6B(T) within the phylum Firmicutes. It is closely related to V. koreensis and V. albus, but with features that clearly distinguish it from species of the genus Virgibacillus or of other related genera. On the basis of the polyphasic evidence derived in this study, we propose that strain B6B(T) be placed within a new genus, as Aquibacillus halophilus gen. nov., sp. nov., with B6B(T) as the type strain ( =IBRC-M 10775(T) =KCTC 13828(T)). We also propose that V. koreensis and V. albus should be transferred to this new genus and be named Aquibacillus koreensis comb. nov. and Aquibacillus albus comb. nov., respectively. The type strain of Aquibacillus koreensis comb. nov. is BH30097(T) ( =KCTC 3823(T) =IBRC-M 10657(T) =JCM 12387(T)) and the type strain of Aquibacillus albus comb. nov. is YIM 93624(T) ( =DSM 23711(T) =IBRC-M 10798(T) =JCM 17364(T)). © 2014 IUMS.

The response of soil biota to phosphate fertilization in grassland columns

NASA Astrophysics Data System (ADS)

Ikoyi, Israel; Winstanley, Henry; Fowler, Andrew; Schmalenberger, Achim

2017-04-01

The United Nations has predicted that food production is expected to rise by 50% in the year 2020 to feed the increasing world population. Grasslands play significant roles in food production and occupy about 70% of the world's agricultural land. However, intensive use of inorganic fertilizers often associated with increased food production can lead to poor soil quality and environmental pollution. For instance, excessive phosphorus (P) application can lead to eutrophication in surface waters. Although P plays vital roles in many metabolic processes in plants, its primary source rock phosphate is finite. Consequently, the development of more P efficient agricultural systems is paramount. P cycling within the microbial biomass is essential to the P cycle within the soil with its key pathways for P mobilization and mineralization from various soil pools into plant available forms. In this study, soil columns were setup in a greenhouse using a P deficient Irish soil (P index 1). The columns were planted with Lolium perenne and fertilized with 0, 5, 10 and 20 kg/ha inorganic P representing control, low, medium and high rates respectively alongside a full complement of other nutrients. Each treatment was replicated six times and managed for 14 weeks. Results after 14 weeks showed that the weekly measurements of phosphate at different soil depths identified only traces of P in soil solution for the duration of 14 weeks, even after P application. There was a significant increase in alkaline and acid phosphatase activities with the high P compared to the control but no significant effect on plant shoot and root biomass, abundances of cultivable calcium phosphate-, phytate- and phosphonate-utilizing bacteria upon P fertilization. L. perenne rhizosphere of the highest P treatment had significantly lower abundance of bacterial phoD genes, mycorrhizal hyphal and arbuscular colonization rates compared to the control. Likewise, the abundance of bacterial- and fungal-feeding nematodes, enrichment index were significantly higher in the control compared to the P treatments. In addition, denaturing gradient gel electrophoresis analysis showed that high and medium P significantly shifted the bacterial, fungal and Glomeromycota community structures compared to the control. The Next Generation Sequencing data revealed that the control had a significantly higher abundance of certain bacterial families when compared to the high P treatment (e.g. Bacillaceae, Paenibacillaceae, Nocardioidaceea, Micrococcaceae, Bradyrhizobiaceae) that have been associated with P mineralization in the past. Our results show that some of the parameters are more sensitive to P application though the effect on others may have been masked by the low P status of the soil. Results from this study suggest that a positive effect of a single inorganic P fertilizer application on plant growth in a soil is largely cancelled out by its negative effect on the soil microbiota. These findings support the hypothesis that soil microbiota play an important role in plant P supply in low P index soils. The findings from this study will be included in a mathematical model on biotic P cycling to better predict the effects of fertilizer application in grassland agriculture.