オカレンス(観察データと標本)

FBIP: Actinobacterial diversity associated with rooibos plants

最新バージョン South African National Biodiversity Institute によって公開 2019/09/30 South African National Biodiversity Institute
Actinobacterial diversity associated with rooibos plants. GenBank accessions KY857826-KY857837

データ レコード

この オカレンス(観察データと標本) リソース内のデータは、1 つまたは複数のデータ テーブルとして生物多様性データを共有するための標準化された形式であるダーウィン コア アーカイブ (DwC-A) として公開されています。 コア データ テーブルには、139 レコードが含まれています。

この IPT はデータをアーカイブし、データ リポジトリとして機能します。データとリソースのメタデータは、 ダウンロード セクションからダウンロードできます。 バージョン テーブルから公開可能な他のバージョンを閲覧でき、リソースに加えられた変更を知ることができます。

ダウンロード

DwC-A形式のリソース データまたは EML / RTF 形式のリソース メタデータの最新バージョンをダウンロード:

DwC ファイルとしてのデータ ダウンロード 139 レコード English で (11 kB) - 更新頻度: unknown
EML ファイルとしてのメタデータ ダウンロード English で (14 kB)
RTF ファイルとしてのメタデータ ダウンロード English で (13 kB)

バージョン

次の表は、公にアクセス可能な公開バージョンのリソースのみ表示しています。

引用方法

研究者はこの研究内容を以下のように引用する必要があります。:

Kirby B (2019): FBIP: Actinobacterial diversity associated with rooibos plants. v1.2. South African National Biodiversity Institute. Dataset/Occurrence. http://ipt.sanbi.org.za/iptsanbi/resource?r=actinobacterial&v=1.2

権利

研究者は権利に関する下記ステートメントを尊重する必要があります。:

パブリッシャーとライセンス保持者権利者は South African National Biodiversity Institute。 This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

GBIF登録

このリソースをはGBIF と登録されており GBIF UUID: cc7bb6e1-3b7e-4b22-a73a-d52fa3a94202が割り当てられています。   South African Biodiversity Information Facility によって承認されたデータ パブリッシャーとして GBIF に登録されているSouth African National Biodiversity Institute が、このリソースをパブリッシュしました。

キーワード

Actinobacteria associated with rooibos plants; Specimen

連絡先

リソースを作成した人:

Bronwyn Kirby
Senior Lecturer
University of Western Cape
Institute for Microbial Biotechnology and Metagenomics, Private Bag X17, Bellville
7535 Cape Town
Western Cape
ZA
0219593033
http://www.imbm.co.za

リソースに関する質問に答えることができる人:

Bronwyn Kirby
Senior Lecturer
University of Western Cape
Institute for Microbial Biotechnology and Metagenomics, Private Bag X17, Bellville
7535 Cape Town
Western Cape
ZA
0219593033
http://www.imbm.co.za

メタデータを記載した人:

Bronwyn Kirby
Senior Lecturer
University of Western Cape
Institute for Microbial Biotechnology and Metagenomics, Private Bag X17, Bellville
7535 Cape Town
Western Cape
ZA
0219593033
http://www.imbm.co.za

他に、リソースに関連付けられていた人:

メタデータ提供者
Mahlatse Kgatla
FBIP Data Specialist
SANBI
2 Cussonia Avenue, Brummeria
0184 Pretoria
Gauteng
ZA
1284351960
http://fbip.co.za/contact/

地理的範囲

Four farms located near Clanwilliam and Citrusdal

座標(緯度経度) 南 西 [-32.019, 18.878], 北 東 [-32.008, 18.911]

生物分類学的範囲

All specimen identified to Species level

Order  Actinomycetales

時間的範囲

開始日 / 終了日 2014-04-08 / 2015-03-15

プロジェクトデータ

Actinobacterial diversity associated with rooibos plants. GenBank accessions KY857826-KY857837

タイトル Actinobacterial diversity associated with rooibos plants
識別子 IBIP-BS13093049874
ファンデイング Foundational Biodiversity Information Programme
Study Area Description Four farms located near Clanwilliam and Citrusdal

プロジェクトに携わる要員:

研究代表者
Bronwyn Kirby

収集方法

Rooibos samples were collected from four farms located near Clanwilliam and Citrusdal – two farms were natural (non-cultivated), organic plants, while the other two were large commercial farms which treated the plants with pesticides (plants were not irrigated). At each site leaves, roots, rhizospheric and bulk soil were collected.Actinobacteria were isolated from soil, leaves and rhizosphere. The number of actinobacteria selected from each site was limited to 100 isolates.In total 1426 actinobacteria were isolated and glycerol stocks have been prepared for all these isolates (stocks are stored in 96 well format). These strains have been stored in the Institute for Microbial Biotechnology and Metagenomic (IMBM) culture collection. Strains were de-replicated based on morphological features and antibiotic activity, which resulted in 139 strains being selected for full polyphasic characterization. Note: The culture collection will be screened in upcoming research projects. In addition, the collection is available for other researchers. The 16S rRNA gene for the 139 strains selected for full characterization isolates were amplified and the isolates were identified to the genus/species level. In highly speciated genera, such as the genus Streptomyces, the 16S rRNA gene lacks the sensitivity to resolve some species relationships. Therefore, for strains where 16S rRNA could not clearly distinguish a strain as being unique (based on phenotypic characteristics) it was decided to amplified the gyrB gene. Metagenomic analysis was very problematic. While it was relatively easy to extract metagenomic DNA from the soil samples, it was very difficult to extract DNA from rooibos leaves. When DNA was extracted the concentration was very low and the 454 amplicon workflow requires 500 ng of input DNA. In addition, the DNA contained PCR inhibitors (likely to be plant phenolics) which inhibited the emulsion PCR. After several months of optimization and one failed pyrosequencing reaction it was decided to rather use the Illumina MiSeq as the metagenomic protocol for this sequencer had just been published. The MiSeq sequencing was successful and based on preliminary data analysis at least 80 000 sequence reads pass quality filters.

Study Extent Four farms located near Clanwilliam and Citrusdal

Method step description:

  1. The project will be undertaken in the Western Cape Province and will be supervised by Drs Kirby and Le Roes-Hill, and conducted by students registered at UWC and CPUT for BSc (Honours) degrees and ND:Biotechnology, respectively. All the equipment, facilities and research expertise for the microbiological part of the project exist within the two research groups. Collaborations have been established with Prof Pieter Gouws (a member of the Rooibos Council) and Prof Jeanine Marnewick, who will assist in sample collection. Culture-based and culture-independent (metagenomic) analyses of the plants and surrounding soils will be conducted, as culture-based techniques only detect a fraction (less than 1%) of the bacterial diversity in an environment [1]. Samples will be collected from several organic and non-organic rooibos farms located within the Cedarberg Region (Citrusdal, Clanwilliam and Niewoudltville). Sampling At each site, approximately 200g of bulk soil will be collected at a depth of 5-10cm for soil analysis (soil particle size, pH, electrical conductivity, total N, total C; which will be conducted at BemLab). Six plants will be sampled at each location. Plants will be carefully removed from the soil to limit disturbance of the roots. Rhizosphere soil will be collected by shaking the root the plants in sterile plastic bags to dislodge the soil loosely associated with the roots. Root samples will also be collected and processed in the laboratory to obtain the rhizospheric soil adhering tightly to the roots. Fresh leaves will be picked from the plants and placed in sterile plastic bags. All samples will be processed within 24 hours of sampling. Isolation and culturing Actinobacteria will be isolated by placing 1 g of soil in 10 ml of sterile distilled water and vortexing vigorously to dislodge the bacteria from the soil particles. The soil suspension will be serially diluted and plated on a selection of agar media known to favour the growth of actinobacteria. All isolation plates will contain cycloheximide to limit fungal growth. For the isolation of endophytic actinobacteria from rooibos leaves, leaves will be surface sterilized with 3% bleach and 70% ethanol, rinsed twice in sterile water. Sterile leaves will be ground up in phosphate buffer using a pestle and mortar; the resulting extract will be serially diluted and plated on plant extract and tap water media [2]. Plates will be incubated at 30°C for up to 8 weeks. Actinobacteria will be identified by colony morphology. Actinobacterial identification The 16S-rRNA gene will be amplified using published protocols. Isolates will be identified to the genus level by BLAST analysis using the EzTaxon-e server [3]. Interesting isolates (i.e. those belonging to rare genera or known PGPRs) will be characterized further. Isolates which represent novel species will be characterised by a full polyphasic taxonomic approach (phylogenetic analysis, phenotypic testing, chemotaxonomic analysis, DNA-DNA hybridization, scanning electron microscopy (SEM) (4,5,6); and their descriptions will be published. Novel isolates will be deposited in curated culture collections (DSMZ and NRRL). SEM will be performed on roots and leaves to visualize actinobacterial mycelium directly associated with plant tissue. Detection of actinobacteria by metagenomic analysis Total metagenomic DNA will be isolated from the soil samples using a soil-DNA isolation kit (ZR Soil Microbe DNA kit; Zymo Research, USA). Actinobacterial 16SrRNA gene sequences will be amplified by nested PCR using universal 16S-rRNA gene PCR primers [7] and actinobacterial-specific 16S-rRNA gene primers [8,9] which have been adapted to include the 454 titanium A/B adaptor sequences. Amplicons generated from several soil/leaf samples will be pooled, sequencing libraries will be generated using Roche 454 LibL kits (unidirectional sequencing) and sequenced on a Roche GS Junior.

追加のメタデータ