scholarly journals Effects of Plant Biomass, Plant Diversity, and Water Content on Bacterial Communities in Soil Lysimeters: Implications for the Determinants of Bacterial Diversity

2007 ◽  
Vol 73 (21) ◽  
pp. 6916-6929 ◽  
Author(s):  
Delita Zul ◽  
Sabine Denzel ◽  
Andrea Kotz ◽  
J�rg Overmann
Keyword(s):  
Species Composition ◽  
Water Content ◽  
Bacterial Diversity ◽  
Plant Species ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Plant Biomass ◽  
Bacterial Species ◽  
Bacterial Community Composition ◽  
Ecological Niches ◽  
Soil Lysimeters

ABSTRACT Soils may comprise tens of thousands to millions of bacterial species. It is still unclear whether this high level of diversity is governed by functional redundancy or by a multitude of ecological niches. In order to address this question, we analyzed the reproducibility of bacterial community composition after different experimental manipulations. Soil lysimeters were planted with four different types of plant communities, and the water content was adjusted. Group-specific phylogenetic fingerprinting by PCR-denaturing gradient gel electrophoresis revealed clear differences in the composition of Alphaproteobacteria, Betaproteobacteria, Bacteroidetes, Chloroflexi, Planctomycetes, and Verrucomicrobia populations in soils without plants compared to that of populations in planted soils, whereas no influence of plant species composition on bacterial diversity could be discerned. These results indicate that the presence of higher plant species affects the species composition of bacterial groups in a reproducible manner and even outside of the rhizosphere. In contrast, the environmental factors tested did not affect the composition of Acidobacteria, Actinobacteria, Archaea, and Firmicutes populations. One-third (52 out of 160) of the sequence types were found to be specifically and reproducibly associated with the absence or presence of plants. Unexpectedly, this was also true for numerous minor constituents of the soil bacterial assemblage. Subsequently, one of the low-abundance phylotypes (beta10) was selected for studying the interdependence under particular experimental conditions and the underlying causes in more detail. This so-far-uncultured phylotype of the Betaproteobacteria species represented up to 0.18% of all bacterial cells in planted lysimeters compared to 0.017% in unplanted systems. A cultured representative of this phylotype exhibited high physiological flexibility and was capable of utilizing major constituents of root exudates. Our results suggest that the bacterial species composition in soil is determined to a significant extent by abiotic and biotic factors, rather than by mere chance, thereby reflecting a multitude of distinct ecological niches.

Changes in Bacterial Species Composition in Enrichment Cultures with Various Dilutions of Inoculum as Monitored by Denaturing Gradient Gel Electrophoresis

1998 ◽  
Vol 64 (12) ◽  
pp. 5046-5048 ◽  
Author(s):  
Colin R. Jackson ◽  
Eric E. Roden ◽  
Perry F. Churchill
Keyword(s):  
Species Composition ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Species ◽  
Enrichment Cultures ◽  
Gradient Gel Electrophoresis ◽  
Enrichment Techniques

ABSTRACT Denaturing gradient gel electrophoresis revealed changes in the bacterial species obtained from enrichment cultures with different inoculum dilutions. This inoculum dilution enrichment approach may facilitate the detection and isolation of a greater number of bacterial species than traditional enrichment techniques.

Effects of Soil Resources on Species Composition, Plant Diversity, and Plant Biomass in an Alpine Meadow, Qinghai-Tibetan Plateau

2008 ◽  
Vol 54 (2) ◽  
pp. 205-222 ◽  
Author(s):  
Changting Wang ◽  
Ruijun Long ◽  
Qilan Wang ◽  
Zengchun Jing ◽  
Yangong Du ◽  
...  
Keyword(s):  
Organic Carbon ◽  
Species Composition ◽  
Plant Species ◽  
Soil Nutrients ◽  
Alpine Meadow ◽  
Plant Biomass ◽  
Belowground Biomass ◽  
Soil Resources ◽  
Aboveground And Belowground Biomass ◽  
Meadow Communities

We investigated the effects of soil resources on species composition, plant diversity, and plant biomass in four alpine Kobresia meadow communities. Species diversity was lower in the Kobresia tibetica swamp meadow community than in the other three communities, but this community was characterized by the highest aboveground and belowground biomass and soil nutrients. Aboveground biomass was positively correlated with soil organic matter and soil total nitrogen in all four alpine meadow communities. The proportion of light fraction organic carbon (LFOC) was positively correlated with soil total organic carbon in all types of grassland. In alpine meadows, belowground biomass mostly occurred at 0-10 cm soil, as did soil nutrients. Community differences in plant species composition were reflected in biomass distribution. The highest total biomass (13,759 ± 497 g/m2) including above- and belowground biomass appeared in the sedge-dominated Kobresia tibetica swamp meadow community. Intermediate biomass (3,235 ± 142 g/m2, 2,645 ± 16 g/m2) was found in the Kobresia pygmaea swamp meadow and Potentilla fruticosa shrubs meadow community, dominated by forbs, sedges, and woody plants. The lowest biomass (2,433 ± 162 g/m2) was observed in the Kobresia humilis meadow, mainly dominated by forbs and grasses. The results indicated that fertility of the vegetation caused a decrease in plant species, increase in plant biomass, and also changes in species composition. Species traits (such as ability to respond to higher nutrient levels) as well as competitive interaction may determine ecosystem function (e.g., productivity). Plants with higher competitive ability would then have access to a greater proportion of available resources, leading to increased total resource uptake by roots, lower nutrient losses from the ecosystems, and increased aboveground and belowground biomass. The distribution of aboveground and belowground biomass is largely influenced by the plant species and growth forms within spatial gradients in soil moisture and edaphic conditions.

Characterization of formulated microbial products by denaturing gradient gel electrophoresis, total cellular fatty acid analysis, and DNA microarray analysis

2008 ◽  
Vol 54 (5) ◽  
pp. 380-390 ◽  
Author(s):  
E. Nowak ◽  
R. Brousseau ◽  
J. Garrett ◽  
L. Masson ◽  
C. Maynard ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Species Composition ◽  
Species Identification ◽  
Dna Microarray ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Species ◽  
Cellular Fatty Acid ◽  
Fatty Acid Analysis ◽  
Gradient Gel Electrophoresis

Two commercial products, Biotize and Cycle, containing bacteria as an active ingredient were characterized for species identification and batch-to-batch variation by denaturing gradient gel electrophoresis (DGGE), total cellular fatty acid analysis (FAA), and a taxonomic DNA microarray. DGGE was useful at assessing the stability of consortia in different batches, and cluster analysis differentiated each batch even when only slight differences in species composition were observed. DGGE, FAA, and DNA microarray results indicated little batch-to-batch variation in Biotize and some batch variation in Cycle. The 3 methods agreed well with species identification in Biotize but generated conflicting results in the species composition of Cycle. This multi-method approach was useful in determining if the observed bacterial species present in the products matched the expected species composition.

DIVERSITY OF CULTURABLE BACTERIAL MICROBIOTA OF THE Eisenia foetida DIGESTIVE TRACT

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

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

scholarly journals Deciphering Substrate-Specific Methane Yields of Perennial Herbaceous Wild Plant Species

Agronomy ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 451
Author(s):  
Moritz von Cossel ◽  
Lorena Agra Pereira ◽  
Iris Lewandowski
Keyword(s):  
Plant Species ◽  
Dry Matter ◽  
Plant Biomass ◽  
Cropping Systems ◽  
Wild Plant ◽  
Small Scale ◽  
Social Ecological ◽  
Wild Plant Species ◽  
Global Demand ◽  
Bioenergy Cropping Systems

The global demand for plant biomass to provide bioenergy and heat is continuously increasing because of a growing interest among many industrialized and developing countries towards climate sound and renewable energy supply. The exacerbation of land-use conflicts proliferates social-ecological demands on future bioenergy cropping systems. Perennial herbaceous wild plant mixtures (WPMs) represent an approach to providing social-ecologically more sustainably produced biogas substrate that has gained increasing public and political interest only in recent years. The focus of this study lies on three perennial wild plant species (WPS) that usually dominate the biomass yield performance of WPM cultivation. These WPS were compared with established biogas crops in terms of their substrate-specific methane yield (SMY) and lignocellulosic composition. The plant samples were investigated in a small-scale mesophilic discontinuous biogas batch test for determining the SMY. All WPS were found to have significantly lower SMY (241.5–248.5 lN kgVS−1) than maize (337.5 lN kgVS−1). This was attributed to higher contents of lignin (9.7–12.8% of dry matter) as well as lower contents of hemicellulose (9.9–11.5% of dry matter) in the WPS. Only minor, non-significant differences to cup plant and Virginia mallow were observed. Thus, when planning WPS as a diversification measure in biogas cropping systems, their lower SMY should be considered.

scholarly journals Photosynthetic parameters of a sedge-grass marsh as a big-leaf: effect of plant species composition

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Markéta Mejdová ◽  
Jiří Dušek ◽  
Lenka Foltýnová ◽  
Lenka Macálková ◽  
Hana Čížková
Keyword(s):  
Species Composition ◽  
Plant Species ◽  
Photosynthetic Parameters ◽  
Acorus Calamus ◽  
Dominant Plant Species ◽  
Local Plant ◽  
Rate Of Photosynthesis ◽  
Carex Acuta ◽  
Leaf P

AbstractThe study estimates the parameters of the photosynthesis–irradiance relationship (PN/I) of a sedge-grass marsh (Czech Republic, Europe), represented as an active “green” surface—a hypothetical “big-leaf”. Photosynthetic parameters of the “big-leaf” are based on in situ measurements of the leaf PN/I curves of the dominant plant species. The non-rectangular hyperbola was selected as the best model for fitting the PN/I relationships. The plant species had different parameters of this relationship. The highest light-saturated rate of photosynthesis (Asat) was recorded for Glyceria maxima and Acorus calamus followed by Carex acuta and Phalaris arundinacea. The lowest Asat was recorded for Calamagrostis canescens. The parameters of the PN/I relationship were calculated also for different growth periods. The highest Asat was calculated for the spring period followed by the summer and autumn periods. The effect of the species composition of the local plant community on the photosynthetic parameters of the “big-leaf” was addressed by introducing both real (recorded) and hypothetical species compositions corresponding to “wet” and “dry” hydrological conditions. We can conclude that the species composition (or diversity) is essential for reaching a high Asat of the “big-leaf ”representing the sedge-grass marsh in different growth periods.

scholarly journals Isolation and efficacy of two bacterial strains antagonists of Erwinia amylovora and Pectobacterium carotovorum

2021 ◽  
Vol 31 (1) ◽  
Author(s):  
M’hamed BENADA ◽  
Boualem BOUMAAZA ◽  
Sofiane BOUDALIA ◽  
Omar KHALADI
Keyword(s):  
Fire Blight ◽  
Erwinia Amylovora ◽  
Bacterial Species ◽  
Crop Protection ◽  
Soft Rot ◽  
Causal Agent ◽  
Plant Diseases ◽  
Ecological Niches ◽  
Pectobacterium Carotovorum ◽  
Bacterial Strains

Abstract Background The development of ecofriendly tools against plant diseases is an important issue in crop protection. Screening and selection process of bacterial strains antagonists of 2 pathogenic bacterial species that limit very important crops, Erwinia amylovora, the causal agent of the fire blight disease, and Pectobacterium carotovorum, the causal agent of bacterial potato soft rot, were reported. Bacterial colonies were isolated from different ecological niches, where both pathogens were found: rhizosphere of potato tubers and fruits and leaves of pear trees from the northwest region of Algeria. Direct and indirect confrontation tests against strains of E. amylovora and P. carotovorum were performed. Results Results showed a significant antagonistic activity against both phytopathogenic species, using direct confrontation method and supernatants of cultures (p<0.005). In vitro assays showed growth inhibitions of both phytopathogenic species. Furthermore, results revealed that the strains of S. plymuthica had a better inhibitory effect than the strains of P. fluorescens against both pathogens. In vivo results on immature pear fruits showed a significant decrease in the progression of the fire blight symptoms, with a variation in the infection index from one antagonistic strain to another between 31.3 and 50%, and slice of potato showed total inhibition of the pathogen (P. carotovorum) by the antagonistic strains of Serratia plymuthica (p<0.005). Conclusion This study highlighted that the effective bacteria did not show any infection signs towards plant tissue, and considered as a potential strategy to limit the fire blight and soft rot diseases.

scholarly journals Relationships between resource availability and elevation vary between metrics creating gradients of nutritional complexity

Oecologia ◽  
2021 ◽  
Vol 195 (1) ◽  
pp. 213-223
Author(s):  
Mark A. Lee ◽  
Grace Burger ◽  
Emma R. Green ◽  
Pepijn W. Kooij
Keyword(s):  
Species Richness ◽  
Plant Species ◽  
Resource Availability ◽  
Plant Biomass ◽  
Plant Species Richness ◽  
Mineral Contents ◽  
Nutritive Values ◽  
Animal Community ◽  
Nutritional Chemistry ◽  
The Relationship

AbstractPlant and animal community composition changes at higher elevations on mountains. Plant and animal species richness generally declines with elevation, but the shape of the relationship differs between taxa. There are several proposed mechanisms, including the productivity hypotheses; that declines in available plant biomass confers fewer resources to consumers, thus supporting fewer species. We investigated resource availability as we ascended three aspects of Helvellyn mountain, UK, measuring several plant nutritive metrics, plant species richness and biomass. We observed a linear decline in plant species richness as we ascended the mountain but there was a unimodal relationship between plant biomass and elevation. Generally, the highest biomass values at mid-elevations were associated with the lowest nutritive values, except mineral contents which declined with elevation. Intra-specific and inter-specific increases in nutritive values nearer the top and bottom of the mountain indicated that physiological, phenological and compositional mechanisms may have played a role. The shape of the relationship between resource availability and elevation was different depending on the metric. Many consumers actively select or avoid plants based on their nutritive values and the abundances of consumer taxa vary in their relationships with elevation. Consideration of multiple nutritive metrics and of the nutritional requirements of the consumer may provide a greater understanding of changes to plant and animal communities at higher elevations. We propose a novel hypothesis for explaining elevational diversity gradients, which warrants further study; the ‘nutritional complexity hypothesis’, where consumer species coexist due to greater variation in the nutritional chemistry of plants.

scholarly journals Microbial Communities, Metabolites, Fermentation Quality and Aerobic Stability of Whole-Plant Corn Silage Collected from Family Farms in Desert Steppe of North China

Processes ◽  
2021 ◽  
Vol 9 (5) ◽  
pp. 784
Author(s):  
Chao Wang ◽  
Lin Sun ◽  
Haiwen Xu ◽  
Na Na ◽  
Guomei Yin ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Diversity ◽  
Fungal Diversity ◽  
North China ◽  
Bacterial Species ◽  
Fungal Species ◽  
Family Farms ◽  
Aerobic Stability ◽  
Whole Plant ◽  
Lactobacillus Kefiri

Whole-plant corn silages on family farms were sampled in Erdos (S1), Baotou (S2), Ulanqab (S3), and Hohhot (S4) in North China, after 300 d of ensiling. The microbial communities, metabolites, and aerobic stability were assessed. Lactobacillusbuchneri, Acinetobacter johnsonii, and unclassified Novosphingobium were present at greater abundances than others in S2 with greater bacterial diversity and metabolites. Lactobacillus buchneri, Lactobacillus parafarraginis, Lactobacillus kefiri, and unclassified Lactobacillus accounted for 84.5%, and 88.2%, and 98.3% of bacteria in S1, S3, and S4, respectively. The aerobic stability and fungal diversity were greater in S1 and S4 with greater abundances of unclassified Kazachstania, Kazachstania bulderi, Candida xylopsoci, unclassified Cladosporium, Rhizopus microspores, and Candida glabrata than other fungi. The abundances of unclassified Kazachstania in S2 and K. bulderi in S3 were 96.2% and 93.6%, respectively. The main bacterial species in S2 were L. buchneri, A. johnsonii, and unclassified Novosphingobium; Lactobacillus sp. dominated bacterial communities in S1, S3, and S4. The main fungal species in S1 and S4 were unclassified Kazachstania, K. bulderi, C. xylopsoci, unclassified Cladosporium, R. microspores, and C. glabrata; Kazachstania sp. dominated fungal communities in S2 and S3. The high bacterial diversity aided the accumulation of metabolites, and the broad fungal diversity improved the aerobic stability.

scholarly journals Effects of Simulated Nitrogen Deposition on the Bacterial Community of Urban Green Spaces

2021 ◽  
Vol 11 (3) ◽  
pp. 918
Author(s):  
Lingzi Mo ◽  
Augusto Zanella ◽  
Xiaohua Chen ◽  
Bin Peng ◽  
Jiahui Lin ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Negative Impact ◽  
Bacterial Community Composition ◽  
N Deposition ◽  
Soil Bacterial Community ◽  
Rrna Gene ◽  
Soil Dna ◽  
Urban Green ◽  
Soil Bacterial

Continuing nitrogen (N) deposition has a wide-ranging impact on terrestrial ecosystems. To test the hypothesis that, under N deposition, bacterial communities could suffer a negative impact, and in a relatively short timeframe, an experiment was carried out for a year in an urban area featuring a cover of Bermuda grass (Cynodon dactylon) and simulating environmental N deposition. NH4NO3 was added as external N source, with four dosages (N0 = 0 kg N ha−2 y−1, N1 = 50 kg N ha−2 y−1, N2 = 100 kg N ha−2 y−1, N3 = 150 kg N ha−2 y−1). We analyzed the bacterial community composition after soil DNA extraction through the pyrosequencing of the 16S rRNA gene amplicons. N deposition resulted in soil bacterial community changes at a clear dosage-dependent rate. Soil bacterial diversity and evenness showed a clear trend of time-dependent decline under repeated N application. Ammonium nitrogen enrichment, either directly or in relation to pH decrease, resulted in the main environmental factor related to the shift of taxa proportions within the urban green space soil bacterial community and qualified as a putative important driver of bacterial diversity abatement. Such an impact on soil life induced by N deposition may pose a serious threat to urban soil ecosystem stability and surrounding areas.

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