Bacterial and fungal community composition across the soil depth profiles in a fallow field

고대근,유가영,윤성택,전성천,정혜근 한국생태학회 2017 Journal of Ecology and Environment Vol.41 No.9

Background: Soil microorganisms play key roles in nutrient cycling and are distributed throughout the soil profile. Currently, there is little information about the characteristics of the microbial communities along the soil depth because most studies focus on microorganisms inhabiting the soil surface. To better understand the functions and composition of microbial communities and the biogeochemical factors that shape them at different soil depths, we analyzed microbial activities and bacterial and fungal community composition in soils up to a 120 cm depth at a fallow field located in central Korea. To examine the vertical difference of microbial activities and community composition, β-1,4-glucosidase, cellobiohydrolase, β-1,4-xylosidase, β-1,4-N-acetylglucosaminidase, and acid phosphatase activities were analyzed and barcoded pyrosequencing of 16S rRNA genes (bacteria) and internal transcribed spacer region (fungi) was conducted. Results: The activity of all the soil enzymes analyzed, along with soil C concentration, declined with soil depth. For example, acid phosphatase activity was 125.9 (± 5.7 (± 1 SE)), 30.9 (± 0.9), 15.7 (± 0.6), 6.7 (± 0.9), and 3.3 (± 0.3) nmol g−1 h−1 at 0–15, 15–30, 30–60, 60–90, and 90–120 cm soil depths, respectively. Among the bacterial groups, the abundance of Proteobacteria (38.5, 23.2, 23.3, 26.1, and 17.5% at 0–15, 15–30, 30–60, 60–90, and 90–120 cm soil depths, respectively) and Firmicutes (12.8, 11.3, 8.6, 4.3, and 0.4% at 0–15, 15–30, 30–60, 60–90, and 90–120 cm soil depths, respectively) decreased with soil depth. On the other hand, the abundance of Ascomycota (51.2, 48.6, 65.7, 46.1, and 45.7% at 15, 30, 60, 90, and 120 cm depths, respectively), a dominant fungal group at this site, showed no clear trend along the soil profile. Conclusions: Our results show that soil C availability can determine soil enzyme activity at different soil depths and that bacterial communities have a clear trend along the soil depth at this study site. These metagenomics studies, along with other studies on microbial functions, are expected to enhance our understanding on the complexity of soil microbial communities and their relationship with biogeochemical factors.

Bacterial and fungal community composition across the soil depth profiles in a fallow field

Ko, Daegeun,Yoo, Gayoung,Yun, Seong-Taek,Jun, Seong-Chun,Chung, Haegeun The Ecological Society of Korea 2017 Journal of Ecology and Environment Vol.41 No.9

Background: Soil microorganisms play key roles in nutrient cycling and are distributed throughout the soil profile. Currently, there is little information about the characteristics of the microbial communities along the soil depth because most studies focus on microorganisms inhabiting the soil surface. To better understand the functions and composition of microbial communities and the biogeochemical factors that shape them at different soil depths, we analyzed microbial activities and bacterial and fungal community composition in soils up to a 120 cm depth at a fallow field located in central Korea. To examine the vertical difference of microbial activities and community composition, ${\beta}$-1,4-glucosidase, cellobiohydrolase, ${\beta}$-1,4-xylosidase, ${\beta}$-1,4-N-acetylglucosaminidase, and acid phosphatase activities were analyzed and barcoded pyrosequencing of 16S rRNA genes (bacteria) and internal transcribed spacer region (fungi) was conducted. Results: The activity of all the soil enzymes analyzed, along with soil C concentration, declined with soil depth. For example, acid phosphatase activity was $125.9({\pm}5.7({\pm}1SE))$, $30.9({\pm}0.9)$, $15.7({\pm}0.6)$, $6.7({\pm}0.9)$, and $3.3({\pm}0.3)nmol\;g^{-1}\;h^{-1}$ at 0-15, 15-30, 30-60, 60-90, and 90-120 cm soil depths, respectively. Among the bacterial groups, the abundance of Proteobacteria (38.5, 23.2, 23.3, 26.1, and 17.5% at 0-15, 15-30, 30-60, 60-90, and 90-120 cm soil depths, respectively) and Firmicutes (12.8, 11.3, 8.6, 4.3, and 0.4% at 0-15, 15-30, 30-60, 60-90, and 90-120 cm soil depths, respectively) decreased with soil depth. On the other hand, the abundance of Ascomycota (51.2, 48.6, 65.7, 46.1, and 45.7% at 15, 30, 60, 90, and 120 cm depths, respectively), a dominant fungal group at this site, showed no clear trend along the soil profile. Conclusions: Our results show that soil C availability can determine soil enzyme activity at different soil depths and that bacterial communities have a clear trend along the soil depth at this study site. These metagenomics studies, along with other studies on microbial functions, are expected to enhance our understanding on the complexity of soil microbial communities and their relationship with biogeochemical factors.

유기물이 시용된 토양에서 Light Fraction-C 함량이 미생물 군집구조에 미치는 영향

이창훈 ( Chang Hoon Lee ),고병구 ( Byong-gu Ko ),박성진 ( Seong-jin Park ),김명숙 ( Myung-sook Kim ),윤순강 ( Sun-gang Yun ) 한국환경농학회 2016 한국환경농학회 학술대회집 Vol.2016 No.-

Soil organic matter could influence soil microbial community and there is a need to investigate the influence compared with some types of organic matter. In this study, we evaluated the effect of rice straw compost and rye amendments on light fraction-C content and the soil microbial community after 8 weeks incubation at 15, 25, 35 ℃. Light fraction C content was negatively correlated to soil respiration. Light fraction-C content in rye application was more the decrease than that of the rice straw compost with increasing incubation temperature. Phospholipid fatty acid analysis(PLFA) indicated that the microbial groups of bacteria, fungi, and total microbial biomass increased due to organic input compared with soil receiving no organic amendments. Increasing temperature decreased total PLFA and abundances of Gram-positive(G+) and Gram-negative(G-) bacteria, and fungi at all treatment amended with rice straw compost and rye application. Also, microbial community structure changed due to the G(+)/G(-) and the fungal to bacterial ratio, which was related to light fraction-C content induced with organic matter inputs and temperature. These results suggested that light fraction-C content could affect the shift of soil microbial community in soil.

Comparative study of the airborne microbial communities and their functional composition in fine particulate matter (PM_2.5) under non-extreme and extreme PM_2.5 conditions

Abd Aziz, Azilah,Lee, Kwangyul,Park, Byeonghyeok,Park, Hongjae,Park, Kihong,Choi, In-Geol,Chang, In Seop Elsevier 2018 Atmospheric environment Vol.194 No.-

<P><B>Abstract</B></P> <P>Asian dust (AD) events increase environmental pollution and have a detrimental effect on human health. Particulate matter with an aerodynamic diameter <2.5 μm (PM<SUB>2.5</SUB>) and containing airborne microorganisms increases during AD events due to the transportation of dust by wind from several arid regions in China. This study analyzed the bacterial and fungal communities associated with average daily PM<SUB>2.5</SUB> concentrations less than (on non-event day: ND) and exceeding (on event day: ED) the air quality standard (36 μg PM<SUB>2.5</SUB> m<SUP>-3</SUP>) set by the Korean government. The taxon compositions and functional genes of airborne microorganisms were assessed using shotgun metagenomics sequencing and metagenome rapid annotation using subsystem technology (MG-RAST) analysis. MG-RAST is an open source web application, serving as a platform that automatically analyzes uploaded metagenomes. During ND, 51% of total bacteria sequences consisted of those from <I>Proteobacteria</I>, which were closely related to nitrogen-fixing bacterial species. A high percentage of functional genes consisted of those genes related to nitrogen metabolism, suggesting that the airborne microorganisms are associated with environmental nitrogen cycles. During ED, 57% of total bacteria sequences consisted of those from <I>Bacteroidetes</I>, accompanied by high relative abundance of sequences from pathogenic species of <I>Bacillus</I> and <I>Staphylococcus</I>. Fungal sequences were mainly composed of those from the phyla <I>Ascomycota</I> and <I>Basidiomycota</I>, which include spore-forming species transported frequently by wind. The abundance of <I>Ascomycota</I> sequences was higher in ED (81%) than in ND (22%) samples, and mainly included those from the plant pathogens <I>Phaeosphaeria</I> and <I>Pyrenophora</I>. These findings indicated that microbial composition shifted from ND to ED samples, even at the phylum level. This switch was likely due to the sources of dust particles, with those during ED being primarily from arid regions in Mongolia and industrial regions in China. Additional studies are required to further understand the diversification of airborne microbial communities in downwind areas.</P> <P><B>Highlights</B></P> <P> <UL> <LI> The bacterial community differed between non-event (ND) and event days (ED). </LI> <LI> <I>Proteobacteria</I> dominated during ND, while <I>Bacteroidetes</I> dominated during ED. </LI> <LI> <I>Ascomycota</I> were highly abundant, especially during ED. </LI> <LI> Several pathogenic genera were identified, and proportion was higher during ED. </LI> <LI> Functional genes related to nitrogen metabolism were abundant during ND. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>

High-Throughput Sequencing Reveals Bacterial Diversity in Raw Milk Production Environment and Production Chain in Tangshan City of China

Huihui Cao,Yanhua Yan,Lei Wang,Lixue Dong,Xueliang Pang,Sining Tang,Aijun Li,Aili Xiang,Litian Zhang,Baiqin Zheng 한국축산식품학회 2021 한국축산식품학회지 Vol.41 No.3

Raw milk is a nature media of microbiota that access milk from various sources, which constitutes a challenge in dairy production. This study characterizes the relationship between the raw milk quality and the bacteria diversity at different sampling sites in dairy farms, aiming to provide a strong scientific basis for good hygienic practices and optimized procedure in milk production. High-throughput sequencing of 16S rRNA V3-V4 region was used to analyze the components, abundance and diversity of 48 bacterial population sampled from 8 different sites in dairy farm: pre-sterilized cow’s teats (C1), post-sterilized cow’s teats (C2), milking cluster (E), milk in storage tank (M1), transport vehicle (M2), storage equipment (E2), cow’s dung samples (F) and drinking water (W). Firmicutes account for predominantly 32.36% (C1), 44.62% (C2), 44.71% (E), 41.10% (M1), 45.08% (M2), 53.38% (F) of all annotated phyla. Proteobacteria accounts for 81.79% in W group and Actinobacteria 56.43% in E2 group. At the genus level, Acinetobacter was the most abundant genus that causes bovine mastitis, Acinetobacter and Arthrobacter were dominant in C1, C2, and E groups, Kocuria in E2 group and Arcobacter in W group. E, C1, and C2 group have very similar bacterial composition, and M1 and M2 demonstrated similar composition, indicating that the milking cluster was polluted by the environment or contact with cow udders. Bacterial population composition in different sampling sites identified by NGS reveals a correlation between the bacteria communities of raw milk production chain and the quality of raw milk.

Effect of temperature treatment on postharvest quality of the cherry tomato (Lycopersicon esculentum var. cerasiforme)

박경민,김효진,김상섭,정문철,박기재,구민선 한국식품저장유통학회 2019 한국식품저장유통학회지 Vol.26 No.6

Heat accumulation in the field accelerates softening and shortens the shelf life of cherry tomatoes. The purpose of this study was to investigate the effect of temperature treatment after harvest on the postharvest quality and microbial communities of cherry tomatoes. Regarding fruit quality properties, a 10℃ treatment after harvest caused a delay in increasing weight loss, firmness, electrolyte leakage and decay rate. After the temperature treatment, an approximately 1-2 log reduction on total viable cells, fungi, Enterobacteriaceae and coliforms was observed in the 10℃ treatment group compared with those at 20 and 30℃. However, total viable cells and decay rate remarkably increased at 10℃ treatment after 26 days. The microbial communities of cherry tomatoes in intitial day after temperature treatment were composed mainly of Staphylococcus xylosus or Bacillus pumilus. During storage, the relative abundance of Staphylococcus xylosus and Bacillus pumilus decreased while Pseudomonas fluorescens, Rahnella aquatilis and Leuconostoc mesenteroid increased during late storage. The rapid increase of total aerobic cells and decay rate in the 10℃ treatment group may be associated with a marked increase in Pseudomonas fluorescens. The results from this study demonstrate the effectiveness of pre-cooling to suppress the softening and indicate an impact on microbial community composition and dynamics during storage.

Vaginal Infections during Pregnancy Increase Breast Milk Microbiome Alpha Diversity and Alter Taxonomic Composition

Azka Ainun Nisaa,Chern-Ein Oon,Sasidharan Sreenivasan,Venugopal Balakrishnan,Deepa Rajendran,Jun-Jie Tan,Fatin Fazrina Roslan,Svetoslav Dimitrov Todorov,Woo-Sik Jeong,Feiyan Zhao,Nur Syafiqah Mohamad 한국식품영양과학회 2023 Preventive Nutrition and Food Science Vol.28 No.1

We previously reported that breast milk from women with (W) or without (WO) vaginal yeast infection during pregnancy differs in its immunological and antimicrobial properties, especially against pathogenic vaginal Candida sp.. Here, we investigated the differences in microbiota profiles of breast milk from these groups. Seventy-two breast milk samples were collected from lactating mothers (W, n=37; WO, n=35). The DNA of bacteria was extracted from each breast milk sample for microbiota profiling by 16S rRNA gene sequencing. Breast milk from the W-group exhibited higher alpha diversity than that from the WO-group across different taxonomic levels of class (P=0.015), order (P=0.011), family (P=0.020), and genus (P=0.030). Compositional differences between groups as determined via beta diversity showed marginal differences at taxonomic levels of phylum (P=0.087), family (P=0.064), and genus (P=0.067). The W-group showed higher abundances of families Moraxellaceae (P=0.010) and Xanthomonadaceae (P=0.008), and their genera Acinetobacter (P=0.015), Enhydrobacter (P=0.015), and Stenotrophomonas (P=0.007). Meanwhile, the WO-group showed higher abundances of genus Staphylococcus (P=0.046) and species Streptococcus infantis (P=0.025). This study shows that, although breast milk composition is affected by vaginal infection during pregnancy, this may not pose a threat to infant growth and development.

Effect of temperature treatment on postharvest quality of the cherry tomato (Lycopersicon esculentum var. cerasiforme)

Kyung Min Park(박경민),Hyo Jin Kim(김효진),Sang Seoup Kim(김상섭),Sang Bong Lee(이상봉),Mooncheol Jeong(정문철),Kee Jai Park(박기재),Minseon Koo(구민선) 한국식품저장유통학회 2019 한국식품저장유통학회지 Vol.26 No.6