scholarly journals The Reaction of Cellulolytic and Potentially Cellulolytic Spore-Forming Bacteria to Various Types of Crop Management and Farmyard Manure Fertilization in Bulk Soil

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 772
Author(s):  
Jakub Dobrzyński ◽  
Paweł Stanisław Wierzchowski ◽  
Wojciech Stępień ◽  
Ewa Beata Górska

The ecology of cellulolytic bacteria in bulk soil is still relatively unknown. There is still only a handful of papers on the abundance and diversity of this group of bacteria. Our study aimed to determine the impact of various crop management systems and farmyard manure (FYM) fertilization on the abundance of cellulolytic and potentially cellulolytic spore-forming bacteria (SCB). The study site was a nearly 100-year-old fertilization experiment, one of the oldest still active field trials in Europe. The highest contents of total carbon (TC) and total nitrogen (TN) were recorded in both five-year rotations. The abundances of SCB and potential SCB were evaluated using classical microbiological methods, the most probable number (MPN), and 16S rRNA Illumina MiSeq sequencing. The highest MPN of SCB was recorded in soil with arbitrary rotation without legumes (ARP) fertilized with FYM (382 colony-forming units (CFU) mL−1). As a result of the bioinformatic analysis, the highest values of the Shannon–Wiener index and the largest number of operational taxonomic units (OTUs) were found in ARP-FYM, while the lowest in ARP treatment without FYM fertilization. In all treatments, those dominant at the order level were: Brevibacillales (13.1–43.4%), Paenibacillales (5.3–36.9%), Bacillales (4.0–0.9%). Brevibacillaceae (13.1–43.4%), Paenibacillaceae (8.2–36.9%), and Clostridiaceae (5.4–11.9%) dominated at the family level in all tested samples. Aneurinibacillaceae and Hungateiclostridiaceae families increased their overall share in FYM fertilization treatments. The results of our research show that the impact of crop management types on SCB was negligible while the actual factor shaping SCB community was the use of FYM fertilization.

1999 ◽  
Vol 65 (8) ◽  
pp. 3526-3533 ◽  
Author(s):  
Dirk Rosencrantz ◽  
Frederick A. Rainey ◽  
Peter H. Janssen

ABSTRACT Most-probable-number (MPN) counts were made of homoacetogenic and other bacteria present in the anoxic flooded bulk soil of laboratory microcosms containing 90- to 95-day-old rice plants. MPN counts with substrates known to be useful for the selective enrichment or the cultivation of homoacetogenic bacteria (betaine, ethylene glycol, 2,3-butanediol, and 3,4,5-trimethoxybenzoate) gave counts of 2.3 × 103 to 2.8 × 105 cells per g of dry soil. Homoacetogens isolated from the terminal positive steps of these dilution cultures belonged to the genus Sporomusa. Counts with succinate, ethanol, and lactate gave much higher MPNs of 5.9 × 105 to 3.4 × 107 cells per g of dry soil and led to the isolation of Desulfovibrio spp. Counting experiments on lactate and ethanol which includedMethanospirillum hungatei in the medium gave MPNs of 2.3 × 106 to 7.5 × 108 cells per g of dry soil and led to the isolation of Sporomusa spp. The latter strains could grow with betaine, ethylene glycol, 2,3-butanediol, and/or 3,4,5-trimethoxybenzoate, but apparently most cells of Sporomusa spp. did not initiate growth in counting experiments with those substrates. Spores apparently accounted for 2.2% or less of the culturable bacteria. It appears that culturableDesulfovibrio spp. and Sporomusa spp. were present in approximately equal numbers in the bulk soil. Multiple, phylogenetically-distinct, phenotypically-different, strains of each genus were found in the same soil system.


Author(s):  
Qingyao Wang ◽  
Songzhe Fu ◽  
Qian Yang ◽  
Jingwei Hao ◽  
Can Zhou ◽  
...  

The estuary is the ecological niche of pathogenic Vibrio spp. as it provides abundant organic and inorganic nutrients from seawater and rivers. However, little is known about the ecology of these Vibrio species in the inland brackish water area. In this study, their co-occurrence and relationships to key environmental constraints (salinity and temperature) in the Hun-Tai River of China were examined using the most probable number polymerase chain reaction (MPN-PCR) approach. We hereby report 2-year continuous surveillance based on six water indices of the Hun-Tai River. The results showed that seawater intrusion maximally reached inland as far as 26.5 km for the Hun-Tai River. Pathogenic Vibrio spp. were detected in 21.9% of the water samples. In particular, V. cholerae, V. parahaemolyticus, and V. vulnificus were isolated in 10 (10.4%), 20 (20.8.5%), and 2 (2.08%) samples, respectively. All V. parahaemolyticus strains were tdh gene negative, 10% were positive for the trh gene. Multi-locus sequence typing (MLST) divided V. parahaemolyticus strains into 12 sequence types (STs) for the Hun-Tai River. Five STs were respectively present in various locations along the Hun-Tai River. The PCR assay for detecting six virulence genes and Vibrio seventh pandemic island I and II revealed three genotypes in 12 V. cholerae isolates. The results of our study showed that seawater intrusion and salinity have profound effects on the distribution of pathogenic Vibrio spp. in the inland river, suggesting a potential health risk associated with the waters of the Hun-Tai River used for irrigation and drinking.


2011 ◽  
Vol 74 (11) ◽  
pp. 1902-1907 ◽  
Author(s):  
CORINNE AUDEMARD ◽  
HOWARD I. KATOR ◽  
MARTHA W. RHODES ◽  
THOMAS GALLIVAN ◽  
A. J. ERSKINE ◽  
...  

In 2009 the U.S. Food and Drug Administration (FDA) announced its intention to implement postharvest processing (PHP) methods to eliminate Vibrio vulnificus from oysters intended for the raw, half-shell market that are harvested from the Gulf of Mexico during warmer months. FDA-approved PHP methods can be expensive and may be associated with unfavorable responses from some consumers. A relatively unexplored PHP method that uses relaying to high salinity waters could be an alternative strategy, considering that high salinities appear to negatively affect the survival of V. vulnificus. During relay, however, oysters may be exposed to rapid and large salinity increases that could cause increased mortality. In this study, the effectiveness of high salinity relay to reduce V. vulnificus to <30 most probable number (MPN) per g and the impact on oyster mortality were assessed in the lower Chesapeake Bay. Two relay experiments were performed during the summer and fall of 2010. Oysters collected from three grow-out sites, a low salinity site (14 to 15 practical salinity units [psu]) and two moderate salinity sites (22 to 25 psu), were relayed directly to a high salinity site (≥30 psu) on Virginia's Eastern Shore. Oysters were assayed for V. vulnificus and Vibrio parahaemolyticus (another Vibrio species of concern) densities at time 0 prior to relay and after 7 and 14 days of relay, using the FDA MPN enrichment method combined with detection by real-time PCR. After 14 days, both V. vulnificus and V. parahaemolyticus densities were ≤0.8 MPN/g, and decreases of 2 to 3 log in V. vulnificus densities were observed. Oyster mortalities were low (≤<4%) even for oysters from the low salinity harvest site, which experienced a salinity increase of approximately 15 psu. Results, although preliminary and requiring formal validation and economic analysis, suggest that high salinity relay could be an effective PHP method.


2021 ◽  
Author(s):  
Philip J Schmidt ◽  
Ellen S Cameron ◽  
Kirsten M Müller ◽  
Monica B Emelko

Diversity analysis of amplicon sequencing data is mainly limited to plug-in estimates calculated using normalized data to obtain a single value of an alpha diversity metric or a single point on a beta diversity ordination plot for each sample. As recognized for count data generated using classical microbiological methods, read counts obtained from a sample are random data linked to source properties by a probabilistic process. Thus, diversity analysis has focused on diversity of (normalized) samples rather than probabilistic inference about source diversity. This study applies fundamentals of statistical analysis for quantitative microbiology (e.g., microscopy, plating, most probable number methods) to sample collection and processing procedures of amplicon sequencing methods to facilitate inference reflecting the probabilistic nature of such data and evaluation of uncertainty in diversity metrics. Types of random error are described and clustering of microorganisms in the source, differential analytical recovery during sample processing, and amplification are found to invalidate a multinomial relative abundance model. The zeros often abounding in amplicon sequencing data and their implications are addressed, and Bayesian analysis is applied to estimate the source Shannon index given unnormalized data (both simulated and real). Inference about source diversity is found to require knowledge of the exact number of unique variants in the source, which is practically unknowable due to library size limitations and the inability to differentiate zeros corresponding to variants that are actually absent in the source from zeros corresponding to variants that were merely not detected. Given these problems with estimation of diversity in the source even when the basic multinomial model is valid, sample-level diversity analysis approaches are discussed.


Author(s):  
B. G. Jega ◽  
O. O. Adebisi ◽  
S. S. Manga

This study aimed to evaluate the impact of abattoir effluent on microbiological quality of the receiving Tagangu River and the susceptibility of the isolates to commonly-used antibiotics. The most probable number (MPN) as well as the Kirby-Bauer method of antibiotic susceptibility test were used and demonstrated the total heterotrophic bacteria as well as Escherichia coli O157:H7 numbers in a total of 30 water samples collected over a period of three months at three strategic points of the river. In accordance with CLSI guidelines, four out of eight bacteria (Enterobacter sp., Pseudomonas aeruginosa, Proteus vulgaris and Citrobacter sp.) isolated, demonstrated multiple antibiotic resistance (MAR) against at least three out of septrin, chloramphenicol, amoxicillin, augmentin, gentamicin, tarivid and streptomycin. All the isolates (Escherichia coli, Klebsiella pneumoniae, Enterobacter sp., Pseudomonas aeruginosa, Proteus vulgaris, Citrobacter sp., Serratia marcescens and Aerobacter aerogenes) showed either high or intermediate susceptibility to sparfloxacin, ciprofloxacin and pefloxacin. The findings indicated that the river has been heavily polluted with the effluent discharges and did not meet any of the WHO guidelines for natural water sources fit for irrigation or other domestic purposes. As such, indiscriminate discharge of abattoir effluent could impact on the microbiological quality and promote increased incidence of multiple antibiotic resistant bacteria in a receiving river.


2020 ◽  
Author(s):  
Jin Li ◽  
Brett Bevers ◽  
Nabila Nafsin ◽  
Qian Liao

<p>Excessive fecal indicator bacteria concentration leads to swimming advisories that are very common to freshwater beaches. To evaluate the concentration and interaction of indicator bacteria in beach sand and water and to examine the factors that affect bacteria concentration, a study was undertaken at Bradford beach, Milwaukee county on the shore of Lake Michigan. In this research, results from monitoring of E. coli and Enterococci in sand and water from Lake Michigan beach were presented. Bacteria counts were obtained using the IDEXX Most Probable Number (MPN) method. An attempt was made to establish a direct ratio of bacteria counts between the two most common eluents used to detach bacteria from sand, i.e., deionized water (DI) and phosphate buffered saline (PBS). The beach sand bacteria count was analyzed using the EPA CANARY event detection software to identify the onset of periods of anomalous water quality. Analysis of beach sand from this study show that for E. coli, it may be possible to establish a relationship between the results generated using two eluents. Results from the model indicates that sand can be a better potential reservoir for indicator bacteria survival than water as a source. The results also show that CANARY may be useful as an early warning system for monitoring beach contamination and may help to identify any abnormal condition very quickly. Also, in this study, the factors that contributed to the high concentration of bacteria resulting in abnormal water quality events are examined which are the impact of Algae in beach water sample and the rainfall effect during the overall month of sampling duration. CANARY software can best indicate the impact of the presence of Algae on bacteria concentration. The analysis of rainfall effect on bacteria concentration was done using statistical software by determining the significance (p-value) between the seasonal mean concentration of E. coli and the mean concentration of E. coli during the sampling duration and from the analyses it is evaluated that rainfall does affect the bacteria concentration. Moreover, the correlation coefficient indicates greater impact of rainfall event on bacteria concentration relative to the presence of Algae level. Regression analysis was also done to estimate the best model that describes the relation between E. coli and water temperature resulting in weak negative linear relationship between the variables.</p>


Weed Science ◽  
2012 ◽  
Vol 60 (3) ◽  
pp. 516-524 ◽  
Author(s):  
L. Jason Krutz ◽  
Robert M. Zablotowicz ◽  
Krishna N. Reddy

A field study was conducted on ans-triazine–adapted soil to determine the effects ofs-triazine exclusion interval (1, 2, 3, or 4 yr), crop production system (continuous corn or continuous soybean), and rhizosphere proximity (bulk or rhizosphere soil) on atrazine degrader populations and activity. Atrazine degrader populations were quantified by a radiological Most Probable Number technique, while degrader activity was assessed via mineralization of ring-labeled14C-atrazine. As thes-triazine exclusion interval increased, atrazine degrader populations declined exponentially, regardless of crop or rhizosphere proximity. Crop and exclusion interval interacted to affect degrader populations (P = 0.0043). Pooled over rhizosphere and bulk soil, degrader populations were 1.5-fold higher and declined 2.8-fold faster in soybean than corn. An interaction between rhizosphere proximity and exclusion interval was also noted (P = 0.0021), whereby degrader populations were 1.9-fold higher and declined 2.8-fold slower in rhizosphere compared with bulk soil, regardless of crop. The time required for 50% mineralization of ring-labeled14C-atrazine (DT50) following exclusion ofs-triazine herbicides increased linearly at a rate of 2.2 d yr−1. In contrast, the DT50for this site prior to a knowns-triazine application was 85 d and declined exponentially over 5 yr of successive atrazine applications: 24.5 d after 1 yr, 10.8 d after two successive years, and 3.8 d after five successive atrazine applications. Omittings-triazines can reduce degrader populations and activity in adapted soils, but more than 4 yr is required to return mineralization kinetics to nonadapted levels, regardless of crop or rhizosphere proximity.


2002 ◽  
Vol 36 (4) ◽  
pp. 513-520 ◽  
Author(s):  
L Egwari ◽  
O O Aboaba

OBJECTIVE: To assess the impact of town planning, infrastructure, sanitation and rainfall on the bacteriological quality of domestic water supplies. METHODS: Water samples obtained from deep and shallow wells, boreholes and public taps were cultured to determine the most probable number of Escherichia coli and total coliform using the multiple tube technique. Presence of enteric pathogens was detected using selective and differential media. Samples were collected during both periods of heavy and low rainfall and from municipalities that are unique with respect to infrastructure planning, town planning and sanitation. RESULTS: Contamination of treated and pipe distributed water was related with distance of the collection point from a utility station. Faults in pipelines increased the rate of contamination (p<0.5) and this occurred mostly in densely populated areas with dilapidated infrastructure. Wastewater from drains was the main source of contamination of pipe-borne water. Shallow wells were more contaminated than deep wells and boreholes and contamination was higher during period of heavy rainfall (p<0.05). E. coli and enteric pathogens were isolated from contaminated supplies. CONCLUSIONS: Poor town planning, dilapidated infrastructure and indiscriminate siting of wells and boreholes contributed to the low bacteriological quality of domestic water supplies. Rainfall accentuated the impact.


2020 ◽  
Vol 2 (7A) ◽  
Author(s):  
Lea Deinert ◽  
Israel Ikoyi ◽  
Achim Schmalenberger

Phosphorus (P) is an essential macronutrient for all living organisms and is applied as fertilizer in agroecosystems to improve crop growth. Recycling-derived fertilizers (RDFs) have been developed for nutrient recovery from Europe’s largest waste streams as a sustainable alternative to this finite resource. The impact of four RDFs (two ashes, two struvites) on the soil microbiome in comparison with a P-free control and triple super phosphate (TSP) as mineral fertilizer was investigated in a pot trial and a subsequent microcosm trial (subset of samples). For both experiments perennial ryegrass was cultivated for 54 days. The pot trial was conducted at P fertilization rates of 20 and 60 kg P ha-1 in quadruplicates. After the pot harvest the bulk soil was stored until the microcosm trial was conducted, using the control, TSP and the two ashes at 60 kg P ha-1 in six replicates. Pot trial results showed highest P bioavailability from struvites at high P rates, also resulting in higher biomass yield on average. Furthermore, P solubilization capabilities from tri-calcium phosphate was enhanced in the RDFs treatments, while the TSP treatments were negatively affected. For the microcosm trial, most probable number (MPN) analysis showed that phytate-utilizing bacterial abundance was significantly increased in one of the ashes and had also remained higher in the RDF treatments after storage. Understanding the effects of recycling-derived fertilizer application on the soil P cycle is vital for developing a more sustainable agriculture.


Author(s):  
Douglas Salome Ibietela ◽  
Alambo, Ayaba Alabo ◽  
Obire, Omokaro

Aim: This study was carried out to compare the bacteriological and physicochemical qualities of boreholes and mono-pumps water samples used as sources of domestic water supply, in Abonnema Community, Akuku-Toru Local Government Area, Rivers State. Methodology: A total of forty-eight water samples were collected twice monthly for four months and evaluated. The bacteriological parameters such as total heterotrophic bacterial, total coliform, faecal coliform, Vibrio, Salmonella - Shigella and Pseudomonas were analyzed using standard microbiological methods.  The coliform was determined using the Most Probable number technique while, the physicochemical parameters were determined using Standard methods for the examination of water and wastewater. Results: The total heterotrophic bacterial, coliform, faecal coliform, Vibrio, Salmonella-Shigella and Pseudomonas counts of the borehole samples ranged from 7.2×102 - 2.4×103, 2.3×102–4.0×102, 3.6×102-4.8×102, 7.3×102-1.4×103, 2.1×102-2.8×102 and 0.0×100Cfu/ml, respectively. The total heterotrophic bacterial counts, coliform counts, faecal coliform counts, Vibrio counts, Salmonella-Shigella counts and Pseudomonas counts for the mono-pump samples ranged from: 1.1×103- 1.8×103, 2.0×102– 9.1×102, 2.4×102- 3.8×102, 4.5×102-8.6×102, 1.4×102 - 4.2×102 and 0.0×100Cfu/ml, respectively. The bacterial genera identified were: Bacillus, Lynsinibacillus, Staphylococcus, Vibrio, Serratia, Enterobacter, Klebsiella, Shigella, Salmonella, Paenibacillus, Aeromonas and Geobacillus. The means of physicochemical parameters for borehole and mono-pump, respectively were: alkalinity: 41.72±0.01-60.85±0.20 and 29.14±0.01-214.87±1.36mg/l; BOD: 8.26±0.01-10.44±0.0 and 5.12±0.01-5.79±0.01; COD: 126.52±0.01-172.41±0.04 and 83.20±0.44-218.00±0.57; DO: 6.31±0.01 and 3.05±0.07-8.29±0.01; calcium: 5.10±0.28-; 4.83±0.00-10.15±0.00 and 2.71±0.00-14.04±0.00; iron: 2.01±0.00-3.37±0.00 and 1.90±0.00-4.73±0.00; lead: 0.38±0.00-1.07±0.00 and 1.24±0.00-1.63±0.00; nitrate: 0.42±0.00-1.08±0.00 and 1.14±0.00-1.75±0.00; zinc:1.10±0.00-3.18±0.00 and 0.39±0.00-1.82±0.00; phosphate: 0.03±0.00-0.13±0.00 and 0.15±0.00-0.87±0.00; pH: 6.54±0.00-7.05±0.07 and 6.29±0.00-6.93±0.01; salinity: 4.02±0.00-5.14±0.00 and 2.83±0.00-5.88±0.00; total organic carbon: 1.39±0.01-2.81±0.010 and 1.64±0.00-3.42±0.01; polycyclic aromatic hydrocarbon: 32.69±0.00-55.73±0.00 and 45.10±0.00-61.49±0.00mg/l; total petroleum hydrocarbon:58.90±0.00-66.15±0.00 and 60.31±0.00-92.11±0.00 mg/l. Conclusion: The high counts of bacterial groups of public health importance identified from this study, including the presence of: COD, DO, Fe, Pb, Phosphate, Zinc, TPH and PAH in high concentrations reveals contamination of the water sources. Thus, treatment before drinking is recommended.


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