scholarly journals Changes in Heterotrophic Picoplankton Community Structure after Induction of a Phytoplankton Bloom under Different Light Regimes

Diversity ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 195 ◽  
Author(s):  
Karayanni ◽  
Kormas ◽  
Moustaka-Gouni ◽  
Sommer
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Relative Abundance ◽  
Environmental Changes ◽  
Phytoplankton Bloom ◽  
Phytoplankton Growth ◽  
Light Regimes ◽  
Operational Taxonomic Units ◽  
Abundant Otus

Bacterial and archaeal diversity and succession were studied during a mesocosm experiment that investigated whether changing light regimes could affect the onset of phytoplankton blooms. For this, 454-pyrosequencing of the bacterial V1-V3 and archaeal V3-V9 16S rRNA regions was performed in samples collected from four mesocosms receiving different light irradiances at the beginning and the end of the experiment and during phytoplankton growth. In total, 46 bacterial operational taxonomic units (OTUs) with ≥1% relative abundance occurred (22–34 OTUs per mesocosm). OTUs were affiliated mainly with Rhodobacteraceae, Flavobacteriaceae and Alteromonadaceae. The four mesocosms shared 11 abundant OTUs. Dominance increased at the beginning of phytoplankton growth in all treatments and decreased thereafter. Maximum dominance was found in the mesocosms with high irradiances. Overall, specific bacterial OTUs had different responses in terms of relative abundance under in situ and high light intensities, and an early phytoplankton bloom resulted in different bacterial community structures both at high (family) and low (OTU) taxonomic levels. Thus, bacterial community structure and succession are affected by light regime, both directly and indirectly, which may have implications for an ecosystem’s response to environmental changes.

Molecular Analysis of Bacterial Community Structure and Diversity in Unimproved and Improved Upland Grass Pastures

1999 ◽  
Vol 65 (4) ◽  
pp. 1721-1730 ◽  
Author(s):  
Allison E. McCaig ◽  
L. Anne Glover ◽  
James I. Prosser
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Sequence Similarity ◽  
Soil Samples ◽  
Operational Taxonomic Units ◽  
16S Ribosomal Dna ◽  
Pcr Products ◽  
Evenness Indices ◽  
Low Coverage

ABSTRACT Bacterial community structure and diversity in rhizospheres in two types of grassland, distinguished by both plant species and fertilization regimen, were assessed by performing a 16S ribosomal DNA (rDNA) sequence analysis of DNAs extracted from triplicate soil plots. PCR products were cloned, and 45 to 48 clones from each of the six libraries were partially sequenced. Phylogenetic analysis of the resultant 275 clone sequences indicated that there was considerable variation in abundance in replicate unfertilized, unimproved soil samples and fertilized, improved soil samples but that there were no significant differences in the abundance of any phylogenetic group. Several clone sequences were identical in the 16S rDNA region analyzed, and the clones comprised eight pairs of duplicate clones and two sets of triplicate clones. Many clones were found to be most closely related to environmental clones obtained in other studies, although three clones were found to be identical to culturable species in databases. The clones were clustered into operational taxonomic units at a level of sequence similarity of >97% in order to quantify diversity. In all, 34 clusters containing two or more sequences were identified, and the largest group contained nine clones. A number of diversity, dominance, and evenness indices were calculated, and they all indicated that diversity was high, reflecting the low coverage of rDNA libraries achieved. Differences in diversity between sample types were not observed. Collector’s curves, however, indicated that there were differences in the underlying community structures; in particular, there was reduced diversity of organisms of the α subdivision of the class Proteobacteria (α-proteobacteria) in improved soils.

Bacterial community diversity and dynamics of Dongzhai harbor mangrove soils in China

2019 ◽  
Vol 65 (10) ◽  
pp. 703-712
Author(s):  
Peng Li ◽  
Siyu Wu ◽  
Haoneng Yin ◽  
Hongping Wu ◽  
Qin Peng ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
High Throughput Sequencing ◽  
Nature Reserve ◽  
Soil Samples ◽  
Community Diversity ◽  
Orthologous Group ◽  
Bacterial Community Diversity ◽  
National Nature Reserve ◽  
Abundant Otus

Dongzhai Harbor National Nature Reserve is the largest mangrove reserve in China, but the bacterial diversity and community structure of soils in the Dongzhai harbor mangrove (DHM) is still not well known. This study was conducted to characterize and compare the bacterial community diversity and composition of DHM soils in three typical sites (YA, entrance of wastewater and sanitary sewage; YB, located in Dongzhai Harbor National Nature Reserve; YC, near the sea) using high-throughput sequencing of the 16S rDNA. Community statistical analyses suggested that the YB and YC soils have a similar community structure, but they differ from the YA soils significantly. Proteobacteria and Chloroflexi were the ubiquitous and dominant groups that made up nearly 80% of total bacterial communities, but it was noted that Chloroflexi had a higher relative abundance in YA soil samples than YB and YC soil samples and that the operational taxonomic units (OTUs) of Anaerolineaceae, Gammaproteobacteria, and Thiogranum reached extremely significant levels. Interaction network analysis of the 50 most abundant OTUs further demonstrated that the OTUs of YA showed few interactions with YB and YC OTUs, and the Cluster of Orthologous Group (COG) involved in lipid transport and metabolism showed significant differences between the YA and YB soil samples. Our results will greatly help to understand the bacterial community variation of the DHM as human activities enhance and grow, and to identify some challenges for the restoration and management of the mangrove ecosystem.

scholarly journals Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress

2016 ◽  
Vol 82 (7) ◽  
pp. 2227-2237 ◽  
Author(s):  
Daiana Lima-Morales ◽  
Ruy Jáuregui ◽  
Amelia Camarinha-Silva ◽  
Robert Geffers ◽  
Dietmar H. Pieper ◽  
...  
Keyword(s):  
Community Structure ◽  
Relative Abundance ◽  
Contaminated Soils ◽  
Catabolic Gene ◽  
The Czech Republic ◽  
Its Gene ◽  
Benzene Toluene ◽  
Gene Structures

ABSTRACTThree types of contaminated soil from three geographically different areas were subjected to a constant supply of benzene or benzene/toluene/ethylbenzene/xylenes (BTEX) for a period of 3 months. Different from the soil from Brazil (BRA) and Switzerland (SUI), the Czech Republic (CZE) soil which was previously subjected to intensivein situbioremediation displayed only negligible changes in community structure. BRA and SUI soil samples showed a clear succession of phylotypes. A rapid response to benzene stress was observed, whereas the response to BTEX pollution was significantly slower. After extended incubation, actinobacterial phylotypes increased in relative abundance, indicating their superior fitness to pollution stress. Commonalities but also differences in the phylotypes were observed. Catabolic gene surveys confirmed the enrichment of actinobacteria by identifying the increase of actinobacterial genes involved in the degradation of pollutants. Proteobacterial phylotypes increased in relative abundance in SUI microcosms after short-term stress with benzene, and catabolic gene surveys indicated enriched metabolic routes. Interestingly, CZE soil, despite staying constant in community structure, showed a change in the catabolic gene structure. This indicates that a highly adapted community, which had to adjust its gene pool to meet novel challenges, has been enriched.

scholarly journals Distribution of antibiotic-resistant bacteria in aerobic composting of swine manure with different antibiotics

2021 ◽  
Vol 33 (1) ◽  
Author(s):  
Tingting Song ◽  
Hongna Li ◽  
Binxu Li ◽  
Jiaxun Yang ◽  
Muhammad Fahad Sardar ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Community Structure ◽  
Bacterial Community ◽  
Relative Abundance ◽  
Bacterial Community Structure ◽  
Swine Manure ◽  
Resistant Bacteria ◽  
Absolute Abundance ◽  
Antibiotic Resistant Bacteria ◽  
Antibiotic Resistant

Abstract Background Livestock manure is an important reservoir of antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs). The bacterial community structure and diversity are usually studied using high-throughput sequencing that cannot provide direct evidence for ARB changes. Thus, little is known about the distribution of ARB, especially in the presence of different antibiotics in composting process. In this study, the fate of ARB was investigated in aerobic composting of swine manure, using chlortetracycline, sulfamethoxazole, lincomycin, and ciprofloxacin as typical antibiotics. The abundance and species of ARB were analyzed systematically to evaluate their ecological risk at different stages of composting. Results The absolute abundance of total ARB decreased, while the relative abundance increased on day 2. The relative abundance of lincomycin-resistant bacteria was higher than other ARBs during the whole composting process. The absolute abundance of four ARBs was 9.42 × 106–2.51 × 102 CFU/g (lincomycin- > chlortetracycline- > sulfamethoxazole- > ciprofloxacin- > multiple antibiotic-resistant bacteria), and they were not completely inactivated at the end of composting. Antibiotics led to a partial proliferation of ARBs including Corynebacterium, Sporosarcina, Solibacillus, and Acinetobacter. Especially, Corynebacterium, a pathogenic genus, was observed in chlortetracycline and lincomycin treatments. Conclusion Among the antibiotics studied, lincomycin showed the highest ecological risk, due to it expanded the range of lincomycin-resistant bacteria at the phyla level (Firmicutes, Actinobacteria, and Proteobacteria). The principal co-ordinates analysis indicated that the bacterial community structure was primarily associated with the composting stages rather than antibiotic types. Possible potential hosts and the related to the decrease of ARGs abundance were indicated based on the network analysis. The decrease of culturable Proteobacteria and the increase of culturable Firmicutes (Solibacillus, Bacillus) partially explained the high degradation rate of various ARGs with the progress of composting in this study. These results provided important information for the control of antibiotic resistance in composting.

scholarly journals Effects of ultraviolet radiation on the community structure and metabolic pathways of A2O process at Plateau environment

2021 ◽  
Author(s):  
Zong Yongchen ◽  
He Qiang ◽  
Guo Mingzhe ◽  
You Junhao ◽  
Zhang Dongyan
Keyword(s):  
Community Structure ◽  
Water Treatment ◽  
Bacterial Community ◽  
Ultraviolet Radiation ◽  
Relative Abundance ◽  
Ultraviolet Irradiation ◽  
Bacterial Communities ◽  
Metabolic Pathways ◽  
Bacterial Community Structure ◽  
Key Species

Abstract Water treatment ecosystem provides important habitats for various bacterial communities. However, the response mechanism of this ecosystem under ultraviolet rays is not yet clear. In the study, 16S rRNA gene sequencing is used to study the bacterial community structure and metabolic pathways under 5 samples of ultraviolet irradiation times. In general, the bacterial communities of the five samples are different, which indicates that the ultraviolet radiation time has an impact on the bacterial community structure. Analysis of driving factors shows that UV, COD, pH, TN and NH3-N have an impact on the relative abundance of key species. Key species under ultraviolet irradiation are Bacteroidetes, Proteobacteria, Actinobacteria, Firmicutes, Chloroflexi, and Chlamydiae, accounting for 96.69%ཞ98.30%, and ultraviolet irradiation has a significant inhibitory effect on the relative abundance. As the dominant bacterial phyla in Plateau environment, Chlamydiae is discovered for the first time. The network co-occurrence diagrams constructed under different ultraviolet radiation show that each sample is composed of three independent network diagrams. There are 6 common dominant phyla and 33 common dominant bacterial genera in each sample, which reveals that the structure of the ecosystem is composed of more similar microorganisms, rather than random phenomena. It also reflects the competitive relationship between species and the adaptability of bacteria to the environment. Through the analysis of metabolic pathways, it is found that the dominant metabolic pathways in high altitude habitats have certain changes under ultraviolet radiation. Further analysis of carbon, nitrogen and phosphorus metabolic pathways shows that the relative abundance of related metabolic pathways has a certain change, but the difference in metabolic maps is small, that is, the effect of ultraviolet radiation is mainly reflected in the relative abundance of metabolic pathways. These findings indicate that ultraviolet radiation in Plateau environment as an important influencing factor has an impact on microbial structure and metabolic pathways. This research provides an important theoretical basis for further understanding of water treatment ecosystem in Plateau environment, and also provides a new perspective for the development of water treatment ecosystem.

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