scholarly journals Genome reduction in an abundant and ubiquitous soil bacterial lineage

2016 ◽  
Author(s):  
Tess E Brewer ◽  
Kim M Handley ◽  
Paul Carini ◽  
Jack A Gibert ◽  
Noah Fierer
Keyword(s):  
Soil Bacteria ◽  
Large Population ◽  
Metabolic Reconstruction ◽  
Soil Environment ◽  
Genomic Databases ◽  
Bacterial Phylotypes ◽  
Bacterial Lineage ◽  
Metabolic Versatility ◽  
Soil Metagenome ◽  
Soil Bacterial

AbstractAlthough bacteria within theVerrucomicrobiaphylum are pervasive in soils around the world, they are underrepresented in both isolate collections and genomic databases. Here we describe a single verrucomicrobial phylotype within the classSpartobacteriathat is not closely related to any previously described taxa. We examined >1000 soils and found this spartobacterial phylotype to be ubiquitous and consistently one of the most abundant soil bacterial phylotypes, particularly in grasslands, where it was typically the most abundant phylotype. We reconstructed a nearly complete genome of this phylotype from a soil metagenome for which we propose the provisional name ‘CandidatusUdaeobacter copiosus’. TheCa. U. copiosus genome is unusually small for soil bacteria, estimated to be only 2.81 Mbp compared to the predicted effective mean genome size of 4.74 Mbp for soil bacteria. Metabolic reconstruction suggests thatCa. U. copiosus is an aerobic chemoorganoheterotroph with numerous amino acid and vitamin auxotrophies. The large population size, relatively small genome and multiple putative auxotrophies characteristic ofCa. U. copiosus suggests that it may be undergoing streamlining selection to minimize cellular architecture, a phenomenon previously thought to be restricted to aquatic bacteria. Although many soil bacteria need relatively large, complex genomes to be successful in soil,Ca. U. copiosus appears to have identified an alternate strategy, sacrificing metabolic versatility for efficiency to become dominant in the soil environment.

scholarly journals Urbanization and Carpobrotus edulis invasion alter the diversity and composition of soil bacterial communities in coastal areas

2020 ◽  
Vol 96 (7) ◽  
Author(s):  
Ana Novoa ◽  
Jan-Hendrik Keet ◽  
Yaiza Lechuga-Lago ◽  
Petr Pyšek ◽  
Johannes J Le Roux
Keyword(s):  
Community Composition ◽  
Bacterial Communities ◽  
Soil Bacteria ◽  
Coastal Dunes ◽  
Coastal Dune ◽  
Western Coast ◽  
Carpobrotus Edulis ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
The Impact

ABSTRACT Coastal dunes are ecosystems of high conservation value that are strongly impacted by human disturbances and biological invasions in many parts of the world. Here, we assessed how urbanization and Carpobrotus edulis invasion affect soil bacterial communities on the north-western coast of Spain, by comparing the diversity, structure and composition of soil bacterial communities in invaded and uninvaded soils from urban and natural coastal dune areas. Our results suggest that coastal dune bacterial communities contain large numbers of rare taxa, mainly belonging to the phyla Actinobacteria and Proteobacteria. We found that the presence of the invasive C. edulis increased the diversity of soil bacteria and changed community composition, while urbanization only influenced bacterial community composition. Furthermore, the effects of invasion on community composition were conditional on urbanization. These results were contrary to predictions, as both C. edulis invasion and urbanization have been shown to affect soil abiotic conditions of the studied coastal dunes in a similar manner, and therefore were expected to have similar effects on soil bacterial communities. Our results suggest that other factors (e.g. pollution) might be influencing the impact of urbanization on soil bacterial communities, preventing an increase in the diversity of soil bacteria in urban areas.

scholarly journals Isolation of Soil Bacteria Adapted To Degrade Humic Acid-Sorbed Phenanthrene

2005 ◽  
Vol 71 (7) ◽  
pp. 3797-3805 ◽  
Author(s):  
D. J. Vacca ◽  
W. F. Bleam ◽  
W. J. Hickey
Keyword(s):  
Humic Acid ◽  
Humic Acids ◽  
Contaminated Soils ◽  
Soil Bacteria ◽  
Polynuclear Aromatic Hydrocarbons ◽  
Aerobic Bacteria ◽  
Substrate Uptake ◽  
Bacterial Phylotypes ◽  
Selective Interaction ◽  
Different Levels

ABSTRACT The goal of these studies was to determine how sorption by humic acids affected the bioavailability of polynuclear aromatic hydrocarbons (PAHs) to PAH-degrading microbes. Micellar solutions of humic acid were used as sorbents, and phenanthrene was used as a model PAH. Enrichments from PAH-contaminated soils established with nonsorbed phenanthrene yielded a total of 25 different isolates representing a diversity of bacterial phylotypes. In contrast, only three strains of Burkholderia spp. and one strain each of Delftia sp. and Sphingomonas sp. were isolated from enrichments with humic acid-sorbed phenanthrene (HASP). Using [14C]phenanthrene as a radiotracer, we verified that only HASP isolates were capable of mineralizing HASP, a phenotype hence termed “competence.” Competence was an all-or-nothing phenotype: noncompetent strains showed no detectable phenanthrene mineralization in HASP cultures, but levels of phenanthrene mineralization effected by competent strains in HASP and NSP cultures were not significantly different. Levels and rates of phenanthrene mineralization exceeded those predicted to be supported solely by the metabolism of phenanthrene in the aqueous phase of HASP cultures. Thus, competent strains were able to directly access phenanthrene sorbed by the humic acids and did not rely on desorption for substrate uptake. To the best of our knowledge, this is the first report of (i) a selective interaction between aerobic bacteria and humic acid molecules and (ii) differential bioavailability to bacteria of PAHs sorbed to a natural biogeopolymer.

scholarly journals Simultaneous Catabolism of Plant-Derived Aromatic Compounds Results in Enhanced Growth for Members of the Roseobacter Lineage

2013 ◽  
Vol 79 (12) ◽  
pp. 3716-3723 ◽  
Author(s):  
Christopher A. Gulvik ◽  
Alison Buchan
Keyword(s):  
Salt Marshes ◽  
Aromatic Compounds ◽  
Soil Bacteria ◽  
Transcript Abundance ◽  
Gene Transcript ◽  
Content Type ◽  
Coastal Salt Marshes ◽  
Metabolic Versatility ◽  
Organic Carbon Pool ◽  
Ruegeria Pomeroyi

ABSTRACTPlant-derived aromatic compounds are important components of the dissolved organic carbon pool in coastal salt marshes, and their mineralization by resident bacteria contributes to carbon cycling in these systems. Members of the roseobacter lineage of marine bacteria are abundant in coastal salt marshes, and several characterized strains, includingSagittula stellataE-37, utilize aromatic compounds as primary growth substrates. The genome sequence ofS. stellatacontains multiple, potentially competing, aerobic ring-cleaving pathways. Preferential hierarchies in substrate utilization and complex transcriptional regulation have been demonstrated to be the norm in many soil bacteria that also contain multiple ring-cleaving pathways. The purpose of this study was to ascertain whether substrate preference exists inS. stellatawhen the organism is provided a mixture of aromatic compounds that proceed through different ring-cleaving pathways. We focused on the protocatechuate (pca) and the aerobic benzoyl coenzyme A (box) pathways and the substrates known to proceed through them,p-hydroxybenzoate (POB) and benzoate, respectively. When these two substrates were provided at nonlimiting carbon concentrations, temporal patterns of cell density, gene transcript abundance, enzyme activity, and substrate concentrations indicated thatS. stellatasimultaneously catabolized both substrates. Furthermore, enhanced growth rates were observed whenS. stellatawas provided both compounds simultaneously compared to the rates of cells grown singly with an equimolar concentration of either substrate alone. This simultaneous-catabolism phenotype was also demonstrated in another lineage member,Ruegeria pomeroyiDSS-3. These findings challenge the paradigm of sequential aromatic catabolism reported for soil bacteria and contribute to the growing body of physiological evidence demonstrating the metabolic versatility of roseobacters.

scholarly journals Impact of Logging and Forest Conversion to Oil Palm Plantations on Soil Bacterial Communities in Borneo

2013 ◽  
Vol 79 (23) ◽  
pp. 7290-7297 ◽  
Author(s):  
Larisa Lee-Cruz ◽  
David P. Edwards ◽  
Binu M. Tripathi ◽  
Jonathan M. Adams
Keyword(s):  
Forest Soil ◽  
Oil Palm ◽  
Bacterial Communities ◽  
Soil Bacteria ◽  
Forest Conversion ◽  
Soil Bacterial Communities ◽  
Oil Palm Plantation ◽  
Β Diversity ◽  
Logged Forest ◽  
Soil Bacterial

ABSTRACTTropical forests are being rapidly altered by logging and cleared for agriculture. Understanding the effects of these land use changes on soil bacteria, which constitute a large proportion of total biodiversity and perform important ecosystem functions, is a major conservation frontier. Here we studied the effects of logging history and forest conversion to oil palm plantations in Sabah, Borneo, on the soil bacterial community. We used paired-end Illumina sequencing of the 16S rRNA gene, V3 region, to compare the bacterial communities in primary, once-logged, and twice-logged forest and land converted to oil palm plantations. Bacteria were grouped into operational taxonomic units (OTUs) at the 97% similarity level, and OTU richness and local-scale α-diversity showed no difference between the various forest types and oil palm plantations. Focusing on the turnover of bacteria across space, true β-diversity was higher in oil palm plantation soil than in forest soil, whereas community dissimilarity-based metrics of β-diversity were only marginally different between habitats, suggesting that at large scales, oil palm plantation soil could have higher overall γ-diversity than forest soil, driven by a slightly more heterogeneous community across space. Clearance of primary and logged forest for oil palm plantations did, however, significantly impact the composition of soil bacterial communities, reflecting in part the loss of some forest bacteria, whereas primary and logged forests did not differ in composition. Overall, our results suggest that the soil bacteria of tropical forest are to some extent resilient or resistant to logging but that the impacts of forest conversion to oil palm plantations are more severe.

Changes in bacterial populations in a clear-cut beech forest soil planted with spruce

1983 ◽  
Vol 29 (6) ◽  
pp. 644-648 ◽  
Author(s):  
Thu Kauri
Keyword(s):  
Organic Matter ◽  
Soil Bacteria ◽  
Forest Type ◽  
Beech Forest ◽  
Ground Vegetation ◽  
Soil Environment ◽  
Bacterial Populations ◽  
Clear Cut ◽  
Clear Cutting ◽  
Multipoint Method

A beech forest after clear-cutting was replanted with spruce. To study how this perturbation affected soil bacteria and their physiological capabilities, an investigation was undertaken 4 years after the change of forest type. Compared with an earlier study in the beech forest, from 1972 to 1975, conducted immediately before clear-cutting, bacterial numbers in the young spruce plantation had increased; an exception was the upper layer (A00), where the numbers decreased. The population densities of bacteria decomposing xylan, pectin, starch, cellulose, and chitin were estimated by a direct multipoint method. The numbers of bacteria in all the physiological groups studied were higher in 1979–1980, with the same exception as before (A00). The greatest changes occurred in the upper horizons. There were considerable changes in the soil environment after the former beech litter fall ceased; the forest floor became more exposed, and the ground vegetation changed. Changes took place in soil properties, such as organic matter and pH. A slight increase in pH was observed in all horizons except in A00, and organic matter increased in two of the horizons (A01/A1; A1).

scholarly journals Diversity of dominant soil bacteria increases with warming velocity at the global scale

2020 ◽  
Author(s):  
Yoshiaki Kanzaki ◽  
Kazuhiro Takemoto
Keyword(s):  
Bacterial Diversity ◽  
Soil Bacteria ◽  
Environmental Changes ◽  
Global Climate ◽  
Aridity Index ◽  
Global Scale ◽  
Soil Bacterial Diversity ◽  
Dominant Soil ◽  
Global Soil ◽  
Soil Bacterial

AbstractUnderstanding global soil bacterial diversity is important because of the key roles soil bacteria play in the global ecosystem. Given the effects of environmental changes (e.g., climate change and human effect) on the diversity of animals and plants, effects on soil bacterial diversity are expected; however, they have been poorly evaluated to date. Thus, in this study, we focused on the soil dominant bacteria because of their global importance and investigated the effects of warming velocity and human activities on their diversity. Using a global dataset of bacteria, we performed spatial analysis to evaluate the effects, while statistically controlling for the potential confounding effects of current climate and geographic parameters with global climate and geographic data. It was demonstrated that the diversity of the dominant soil bacteria was influenced globally by warming velocity (showing significant increases) in addition to aridity index (dryness) and pH. The effects of warming velocity were particularly significant in forests and grasslands. An effect from human activity was also observed, but it was secondary to warming velocity. These findings provide robust evidence, and advance our understanding of the effects of environmental changes (particularly global warming) on soil bacterial diversity at the global scale.

scholarly journals Intimate relationships among soil bacteria: actinomycetes and mycolic acid-containing bacteria

2021 ◽  
Author(s):  
Manami Kato ◽  
Shumpei Asamizu ◽  
Hiroyasu Onaka
Keyword(s):  
Intimate Relationships ◽  
Soil Bacteria ◽  
Liquid Culture ◽  
Mycolic Acid ◽  
Metabolic Changes ◽  
Natural Soil ◽  
Selective Screening ◽  
Soil Environment ◽  
Aggregate Form ◽  
Single Strain

Abstract Co-culture is an efficient strategy for natural product discovery. We have used mycolic acid-containing bacteria (MACB) Tsukamurella pumonis TP-B0596 to induce secondary metabolism by actinomycetes and have found several natural products. We also observed that MACB attached to the mycelium of Streptomyces lividans forming coaggregates during combined-culture. This stimulated interest in the interactions among actinomycetes and MACB, and we found that soil isolated cultures contained a mixture of actinomycetes and MACB. Our previously observed interactions were the result of selective screening and combination of bacteria in the lab, which warranted investigation of the existence of these interactions in the natural soil environment. Therefore, in this paper, we report the interaction between a co-isolated natural pair of actinomycetes and MACB in terms of morphology and metabolic changes. A natural pair of actinomycetes and MACB co-aggregated in liquid culture and showed metabolic changes. Interestingly, co-aggregated actinomycetes and MACB were re-isolated from soil with no obvious morphological colony differences from the colony of a single strain. The results demonstrate that there is a stochastic chance of picking colonies containing co-aggregated actinomycetes and MACB, which suggests that the pair can exist in co-aggregate form in the soil environment and interact with each other.

scholarly journals Heterogeneity of Soil Bacterial and Bacteriophage Communities in Three Rice Agroecosystems and Potential Impacts On Nutrient Cycling

2022 ◽  
Author(s):  
Yajiao Wang ◽  
Yu Liu ◽  
Yuxing Wu ◽  
Nan Wu ◽  
Wenwen Liu ◽  
...  
Keyword(s):  
Community Structure ◽  
Nutrient Cycling ◽  
Soil Bacteria ◽  
Southern China ◽  
Eastern China ◽  
Soil Microbial Communities ◽  
Illumina Miseq ◽  
Metagenomic Sequencing ◽  
Soil Bacterial Diversity ◽  
Soil Bacterial

Abstract Background: As genetic entities infecting and replicating only in bacteria, bacteriophages can regulate the community structure and functions of their host bacteria, but they are often overlooked because of their relatively low abundance. The ecological roles of bacteriophages in aquatic and forest environments have been widely explored, but those in agroecosystems remains limited. Here, we used metagenomic sequencing to analyze the diversity and interactions of bacteriophages and their host bacteria in soils from three typical rice agroecosystems in China: double cropping in Guangzhou, southern China, rice–wheat rotation cropping in Nanjing, eastern China and early maturing single cropping in Jiamusi, northeastern China. Bacteriophages were isolated and their functions on soil nitrogen cycling and effect on soil bacterial community structure were verified in pot inoculation experiments and Illumina MiSeq sequencing.Results: Soil bacterial and viral diversity and functions varied among the three agroecosystems. Genes detected in communities from the three agroecosystems were associated with typical functions; soil bacteria in Jiamusi were significantly enriched in genes related to carbohydrate metabolism, in Nanjing with xenobiotics biodegradation and metabolism, and in Guangzhou with virulence factors and scarce in secondary metabolite biosynthesis, which might lead to a significant occurrence of rice bacterial diseases. In the three ecosystems, 368 species of virus were detected. Notably, over-represented auxiliary carbohydrate-active enzyme (CAZyme) genes were identified in the viruses, which might assist host bacteria in metabolizing carbon, and 67.43% of these genes were present in Jiamusi. In bacteriophage isolation and inoculation experiments, Enterobacter bacteriophage-NJ reduced the nitrogen fixation capacity of soil by lysing N-fixing host bacteria and changed the soil bacterial diversity and community structure.Conclusions: Our results showed that diversity and function of paddy soil bacteria and viruses varied in the three agroecosystems. Soil bacteriophages can affect nutrient cycling by expressing auxiliary metabolic genes (AMGs) and lysing the host bacteria that are involved in biogeochemical cycles. These findings form a basis for better understanding bacterial and bacteriophage diversity in different rice agroecosystems, laying a solid foundation for further studies of soil microbial communities that support ecofriendly production of healthy rice.

scholarly journals Consistent effects of vegetation loss on abundant and rare soil microbial phylotypes across nitrogen-enrichment levels

2019 ◽  
Author(s):  
Dima Chen ◽  
Ying Wu ◽  
Muhammad Saleem ◽  
Bing Wang ◽  
Shuijin Hu ◽  
...  
Keyword(s):  
Soil Bacteria ◽  
Alpha Diversity ◽  
N Deposition ◽  
Bacterial Phylotypes ◽  
Soil Microbial ◽  
N Enrichment ◽  
Soil Bacteria And Fungi ◽  
Bacteria And Fungi ◽  
Vegetation Loss ◽  
First Time

Abstract Soil harbors highly diverse abundant and rare microbial phylotypes that drive multiple soil functions. Given increasing intensity and frequency of vegetation loss and anthropogenic reactive nitrogen (N) inputs to the soil in the future, we lack a mechanistic understanding of how vegetation loss may influence abundant and rare microbial phylotypes at various N-enrichment levels. In the current study, we assessed the effects of vegetation loss on abundant and rare phylotypes of soil bacteria and fungi across three N-enrichment levels in a semi-arid grassland ecosystem. After six years of experimentation in with and without vegetation plots, the vegetation loss increased the total relative abundance of abundant soil bacterial phylotypes but not that of abundant fungal phylotypes at across N-enrichment levels. It is very likely because the number of abundant bacterial phylotypes with positive than negative responses to vegetation loss was higher; however, the number of abundant fungal phylotypes with positive than negative responses to vegetation loss was similar during this period. Moreover, the vegetation loss did not alter the alpha-diversity of abundant or rare bacterial phylotypes, or, of abundant fungal phylotypes; however, it reduced the alpha-diversity of rare fungal phylotypes at across N-enrichment levels. The vegetation loss, however, altered the beta-diversity of abundant and rare bacterial and fungal phylotypes across N-enrichment levels. We found that, against expectations, the effects of vegetation loss on the diversity of abundant and rare phylotypes of both bacteria and fungi were relatively consistent across N-enrichment levels. Our findings provide, for the first time, the phylotype-based data on how vegetation loss affects abundant and rare phylotypes of soil bacteria and fungi across N-enrichment levels. The results also indicate that the effects of vegetation loss on belowground functions may be relatively insensitive to the differences in the N-deposition rates.

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