Marine macrophytes (seagrasses and macroalgae) and their epiphytic microorganisms play an important role in the ecological and biochemical processes of coastal oceans. However, simultaneous ...comparative studies on the biodiversity and functions of epiphytic bacteria and fungi associated with marine macrophytes have not been conducted. In this study, high-throughput sequencing technology was used to describe the epiphytic bacterial and fungal communities of 11 common macroalgae and 2 seagrasses from an intertidal zone of northern China and compare them with seawater communities. The results showed that Proteobacteria and Bacteroidota were the dominant bacterial phyla in marine macrophytes, whereas Ascomycota, Chytridiomycota, and Basidiomycota were the dominant fungal phyla. The alpha diversity of the bacterial and fungal communities in seagrasses was the highest of all macrophyte samples. This may have been related to their ability to recruit microorganisms from multiple sources. Host phylogeny may influence bacterial community structure, and geographical differences may influence fungal community structure. The FAPROTAX data indicated that C metabolic microbes were enriched in marine macrophytes, while the FUNGuild data indicated that undefined saprotroph, which participated in organic matter degradation, were also enriched in marine macrophytes. These findings provide a theoretical basis regarding the epiphytic microorganisms of macrophytes and may offer new insights to support the improved ecological restoration of seagrass and macroalgae beds.
Husain DA, Aziz ZS. 2021. Short Communication: Molecular study of bacteria isolated from meat and chicken frozen from Misan Governorate market in Iraq. Biodiversitas 23: 81-86. Food contamination is ...frequently defined as spoiled or tainted foods because they contain microorganisms, such as fungi, bacteria, parasites, or toxic substances that make them unfit for consumption. In this study, one hundred meat and chicken Frozen products samples were collected randomly from the commercial markets in Misan Governorate, Iraq from November 2020 to April 2021, included: (burger – sausage – kebab – shawarma – minced meat) of meat and (chest-thigh-liver-burger-kebab) of Chicken. The results of aerobic plate count showed that all meat and chicken products were contaminated with bacteria, but the imported products were more contaminated than the local products. Our study included the isolation and diagnosis of eighteen bacterial species by using routine and standard bacteriological tests. The results showed that Gram-negative bacteria were common in meat products (52%) and Gram-positive bacteria represented 48%. In chicken samples, the Gram-positive bacteria was most dominant (59%) while the percentage of Gram-negative bacteria was 41%. Monoplex PCR was used to identify eighteen bacterial strains using a universal 16S rRNA primer that gave 1500 bp amplification product, nucleotide sequences were studied at the National Center for Biotechnology Information (NCBI) using the Basic Local Alignment Search Tool (Nucleotide BLAST). The diagnosed bacteria were Aeromonas veronii, Pseudomonas plecoglossicida, Acinetobacter lwofii, Aeromonas veronii, Klebsiella pneumoniae, Pseudomonas japonica, Pseudomonas songnenensis, Klebsiella pneumoniae subsp. ozaenae, Psychrobacter sanguinis, Klebsiella pneumoniae strain, Acinetobacter lwofii, Lysinibacillus boronitolerans, Bacillus licheniformis, Enterobacter hormaechei, Pseudomonas putida strain, Serratia liquefaciens strain, Comamonas testosterone strain, and Methylogaea oryzae strain which recorded in the Gene Bank belong to different accession numbers.
The role of plant growth-promoting rhizobacteria (PGPR) in adaptation of plants in extreme environments is not yet completely understood. For this study native bacteria were isolated from ...rhizospeheric arid soils and evaluated for both growth-promoting abilities and antagonistic potential against phytopathogenic fungi and nematodes. The phylogentic affiliation of these representative isolates was also characterized. Rhizobacteria associated with 11 wild plant species from the arid soil of Almadinah Almunawarah, Kingdom of Saudi Arabia (KSA) were investigated. From a total of 531 isolates, only 66 bacterial isolates were selected based on their ability to inhibit Fusarium oxysporum, and Sclerotinia sclerotiorum. The selected isolates were screened in vitro for activities related to plant nutrition and plant growth regulation as well as for antifungal and nematicidal traits. Isolated bacteria were found to exhibit capabilities in fix atmospheric nitrogen, produce ammonia, indoleacetic acid (IAA), siderophores, solubilize phosphate and zinc, and showed an antagonistic potential against some phytopathogenic fungi and one nematode species (Meloidogyne incognita) to various extent. Isolates were ranked by their potential ability to function as PGPR. The 66 isolates were genotyped using amplified rDNA restriction analysis (ARDRA) and 16S rRNA gene sequence analysis. The taxonomic composition of the representative genotypes from both rhizosphere and rhizoplane comprised Bacillus, Enterobacter and Pseudomonas. Out of the 10 genotypes, three strains designated as PHP03, CCP05, and TAP02 might be regarded as novel strains based on their low similarity percentages and high bootstrap values. The present study clearly identified specific traits in the isolated rhizobacteria, which make them good candidates as PGPR and might contribute to plant adaption to arid environments. Application of such results in agricultural fields may improve and enhance plant growth in arid soils.
In recent years, there has been an unprecedented advancement in
in situ
analytical approaches that contribute to the mechanistic understanding of microbial communities by explicitly incorporating ...ecology and studying their assembly. In this study, we have analyzed the temporal profiles of the healthy broiler cecal microbiome from day 3 to day 35 to recover the stable and varying components of microbial communities. During this period, the broilers were fed three different diets chronologically, and therefore, we have recovered signature microbial species that dominate during each dietary regime. Since broilers were raised in multiple pens, we have also parameterized these as an environmental condition to explore microbial niches and their overlap. All of these analyses were performed in view of different parameters such as body weight (
BW-mean
), feed intake (
FI
), feed conversion ratio (
FCR
), and age (
days
) to link them to a subset of microbes that these parameters have a bearing upon. We found that gut microbial communities exhibited strong and statistically significant specificity for several environmental variables. Through regression models, genera that positively/negatively correlate with the bird’s age were identified. Some short-chain fatty acids (SCFAs)-producing bacteria, including
Izemoplasmatales
,
Gastranaerophilales
, and
Roseburia
, have a positive correlation with age. Certain pathogens, such as
Escherichia-Shigella
,
Sporomusa
,
Campylobacter
, and
Enterococcus
, negatively correlated with the bird’s age, which indicated a high disease risk in the initial days. Moreover, the majority of pathways involved in amino acid biosynthesis were also positively correlated with the bird’s age. Some probiotic genera associated with improved performance included
Oscillospirales
;
UCG-010
,
Shuttleworthia
,
Bifidobacterium
, and
Butyricicoccaceae
;
UCG-009
. In general, predicted antimicrobial resistance genes (piARGs) contributed at a stable level, but there was a slight increase in abundance when the diet was changed. To the best of the authors’ knowledge, this is one of the first studies looking at the stability, complexity, and ecology of natural broiler microbiota development in a temporal setting.
The rhizosphere, i.e. the interface between plant roots and soil, harbors complex bacterial communities that can influence plant growth. Different plant species can have a distinct influence on the ...bacterial assembly. However, genetic traits found in the same plant species, i.e. different plant genotypes, can also drive bacterial communities in rhizosphere. In this study, bacterial communities in a sandy soil (Fluvisol) and rhizosphere of four lima bean (Phaseolus lunatus) genotypes were assessed by 16S rRNA gene sequencing. In general, Proteobacteria (23.3%), Actinobacteria (20.6%) and Firmicutes (12%) were the most dominant phyla in all samples. We found a distinct microbial structure between genotypes and bulk soil, with an increase of Proteobacteria and Actinobacteria, and a decrease of Firmicutes in the rhizosphere compared to the bulk soil. Also, the results showed that different biological and chemical drivers of each lima bean genotype influenced bacterial structure. Interestingly, each genotype enriched specific microbial taxa in rhizosphere. Our data revealed that plants influenced bacterial assembly in rhizosphere even at a genotype level. The findings gathered in this study can contribute to identify some specific bacterial groups associated with distinct genotypes of lima bean and can drive further studies about the contribution of these bacterial groups on lima bean growth.
•Lima bean genotypes enriched specific microbial taxa in the rhizosphere.•Plants influenced bacterial assembly in rhizosphere even at a genotype level.•High taxonomical level showed a microbial core among lima bean cultivars.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Cadmium (Cd) contamination seriously threatens the soil health and food safety. Combination of amendment and accumulator plant is a green and effective technique to improve phytoremediation of ...Cd-contaminated alkaline soil. In this study, a potting experiment was conducted to investigate the effect of sulfur on Cd phytoextraction by Cichorium intybus (chicory). Soil chemical and microbial properties were determined to reveal the mechanism of sulfur-assisting Cd phytoremediation by chicory. Soil pH decreased from 7.77 to the lowest 7.30 with sulfur addition (0.6, 0.9 and 1.2 g kg−1, LS, MS and HS treatment); Electric conductivity, sulfate anion and available cadmium concentration increased gradually with increasing sulfur doses. Cd concentration of shoot and root significantly increased from 1.47 to 4.43 mg kg−1, 6.15 to 20.16 mg kg−1 by sulfur treatment relative to CK, which were attributed to increased available Cd concentration induced by decreased pH. Sulfur treatments significantly increased the Cd bioconcentration factor by 64.1%, 118.6%, 201.0% for shoot, 76.3%, 145.6% and 227.7% for root under LS, MS and HS relative to CK treatment, respectively (P < 0.05). However, only MS treatment significantly improved the Cd removal efficiency by 82.9% in comparison of CK treatment (P < 0.05). Microbial community diversity measured by 16SrRNA showed that Thiobacillus and Actinobacteria were the key and dominant strains of soil microbial communities after sulfur addition, which played a pivotal role in the process of sulfur oxidation involved in decrease of soil pH and the transformation of Cd forms. Correlation analysis and path analysis by structural equation model indicated that soil sulfate anion and Thiobacillus directly affected Cd removal efficiency by chicory in Cd-contaminated alkaline soil. This suggests that combination of sulfur and chicory may provide a way to promote Cd bioaccumulation for phytoremediation of Cd-contaminated alkaline soil.
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•Addition of sulfur resulted in decreased soil pH and increased sulfate anion, available Cd and exchangeable Cd.•Sulfur application in the alkaline soil increased Cd accumulation in chicory.•Thiobacillus and Actinobacteria are the key and dominant strains in the process of sulfur oxidation.•Carbonate-bound Cd showed remarkable relationship with shoot and root bioconcentration factor of Cd in chicory.•Sulfate anion directly affected removal efficiency of Cd from alkaline soil by Chicory.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Plant-soil interactions play an important role in regulating C cycling in soils, with their management representing a potential means to regulate CO2 emissions and storage of C as soil organic matter ...(SOM). Therefore, crop selection, explicitly targeting beneficial plant-soil interactions may be a tool for sustainable agriculture and to support the maintenance of soil health, particularly in grassland systems which are important known stores of C. However, there is a need to understand whether the selection of different grass species and varieties can control the rates and products of C cycling, and the extent to which this is driven by the interaction with below ground microbial communities. In this study we used controlled environment microcosms to determine the emission of CO2, mineralization of soil organic matter (SOM) and plant driven microbial community selection from soil planted with one of 10 different grasses, representing 2 varieties from 5 different grass species. Total CO2 emissions significantly varied between soil planted with different grasses, with species explaining 43 % of the variation in CO2 emissions and variety 10 %. SOM mineralization and the composition of the microbial community as characterised by 16SrRNA gene profiling was also found to vary between soils planted with different grasses. Root biomass was a significant predictor (r2 = 0.17, P < 0.005) of total CO2 emissions, but not soil organic matter mineralization, while microbial community composition was found to explain 9 % of CO2 emissions. These results suggest that there is the potential to mitigate the production of CO2 from grasslands through the selection of grass varieties that promote the immobilization of C rather than its emission as CO2 and that this is both a function of plant traits and the soil microbial community.
•CO2 efflux from soils varied with the grass variety planted.•SOM mineralization also varied with the grass variety planted.•The soil microbiome explained 9 % of the variation in CO2 efflux.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The identification of effective indigenous strains of Bradyrhizobia could lead to the development of efficient and affordable inoculants for improving soil fertility. This can also promote nitrogen ...fixation in smallholder farming systems of Nigeria and as well make the use of nitrogen fertilizers unnecessary. This study was conducted to characterize and evaluate the nodulating properties of indigenous Bradyrhizobium species in soybean plant. A total of 18 strains were isolated using Bradyrhizobium japonicum selective medium (BJSM) from the root nodules of plants harvested from five sites on Ahmadu Bello University farm, Zaria Kaduna State, Nigeria. These isolates were evaluated for nodulating potential in a screen house using soybean (TGx 1448-2E) as a test crop. The total number of nodules, percentage effective nodules, nodule fresh and dry weights, shoot fresh and dry weight and plant nitrogen content were assessed. The nodules produced by the isolates showed high percentage effectiveness with isolate A4 having significantly higher nodule dry weight (78.00 mg) than the rest of the test isolates. The soybean inoculant, BIOFIX used in this study performed poorly having a nodule dry weight of 6.0 mg. There was positive and highly significant correlation between the nodule dry weight, shoot dry weight and plant nitrogen content (r=0.740, 0.641, 0.616, respectively) at p<0.001. Sequence analyses were carried out on the high performing isolates from each site of sampling and the result obtained using the NCBI Database showed similarity of these isolates with reference strains belonging to the genus Bradyrhizobium (A4- Bradyrhizobium japonicum RV9, B2- Bradyrhizobium guangdongense CCBAU 51649, C1- Bradyrhizobium sp. UFLA05-149, D3- Bradyrhizobium sp. B918 and E3- Bradyrhizobium sp.UFLA05-149). A 16srRNA phylogenetic tree constructed with the sequences obtained grouped the isolates without any close reference strain. However, isolate B2 showed close affiliation with Bradyrhizobium guagdongense with 95% sequence identity. Based on the effectiveness of these five strains of Bradyrhizobium, it is suggested that they can be used as potential candidate for inoculants production.
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