Numerical taxonomy and ecology of oligotrophic bacteria isolated from the estuarine environment

1977 ◽  
Vol 23 (6) ◽  
pp. 733-750 ◽  
Author(s):  
L. M. Mallory ◽  
B. Austin ◽  
R. R. Colwell

Slow-growing bacteria, isolated on nutrient-rich and nutrient-limited media, from Chesapeake Bay water and sediment samples, were examined for 119 biochemical, cultural, morphological, nutritional, and physiological characters. Those bacteria which grow on low nutrient media, termed oligotrophs, a total of 162 strains, were subjected to taxonomic analysis, as a preliminary step in determining their ecological significance. The data for all strains included in the study were examined by computer and the simple matching (SSM) and Jaccard (SJ) coefficients calculated. Clustering was achieved by the unweighted average-linkage method. From sorted similarity matrices and dendrograms, 148 strains, 90% of the total, were recovered in 24 phenetic groups defined at the 80 to 85% similarity level. Only 12 phena could be presumptively identified and these included representatives of Alcaligenes, Corynebacterium, Hyphomicrobium, Hyphomonas polymorpha. Listeria, Nocardia marina, Pedomicrobium, Planococcus citreus, Sphaerotilus, Streptothrix, and Streptomyces. Of the remaining organisms, 10% were unidentified sheathed bacteria. It is concluded that slow-growing bacteria are distributed throughout the estuarine environment and can account for a large proportion of the colonies observed on media after prolonged periods of incubation. The oligotrophic bacteria appear to predominate in areas where the concentration of available nutrients is low and are more characteristic of non-eutrophic aquatic systems.

1977 ◽  
Vol 23 (10) ◽  
pp. 1433-1447 ◽  
Author(s):  
B. Austin ◽  
D. A. Allen ◽  
A. L. Mills ◽  
R. R. Colwell

A total of 230 strains of metal-tolerant bacteria from water and sediment samples collected in Chesapeake Bay were isolated on a medium containing cobalt, lead, mercury, or molybdenum. In addition, a set of 71 cultures were simultaneously isolated on glucose tryptone yeast extract agar medium without metals. Twenty-three reference strains were also included in the numerical taxonomy study of these bacteria, bringing the grand total of strains examined to 324. All strains were examined for 112 biochemical, cultural, morphological, and physiological characters. The taxonomic data obtained were analyzed by computer and the simple matching (SSM) and Jaccard (SJ) coefficients were calculated. Clustering achieved by unweighted average linkage is presented and. from sorted similarity matrices and dendrograms, 294 strains, i.e., 97% of the total, were recovered in 12 phenetic groups defined at the 75 to 80% similarity level. Among the strains there were nine phena presumptively identified as Bacillus, Erwinia, Mycobacterium, Pseudomonas, and coryneforms. From the results of the taxonomic study, it is concluded that metal tolerance in estuarine water and sediment bacteria occurs among a restricted range of taxa distributed throughout the estuarine environment.


Jurnal INFORM ◽  
2019 ◽  
Vol 4 (2) ◽  
Author(s):  
Sulthan Fikri Mu'afa ◽  
Nurissaidah Ulinnuha

Livestock products are widely used by the community in their daily lives, for example as food ingredients, industrial material sources, labor resources, fertilizer sources and energy sources. This study aims to cluster livestock potential with data on livestock population in Sidoarjo Regency in 2017 with single linkage, complete linkage and average linkage method and comparing performance of the methods. In this cluster, the data will be grouped into 3 clusters. The results of the three clusters were obtained by sixteen sub-districts in the first cluster with the potential for low livestock and each one in the second and third clusters for single linkage and average linkage. While complete linkage obtained fifteen sub-districts in the first cluster with high potential for livestock, two sub-districts in the second cluster with the potential of medium livestock and one sub-district in the third cluster with the potential for high farm animals. In the comparison of the standard deviation ratio value, the smallest value of 0.222 is obtained by complete linkage, which shows that complete linkage is better than single linkage and average linkage in the case of subgrouping based on Sidoarjo regency livestock types.


2019 ◽  
Vol 8 (4) ◽  
pp. 486-495
Author(s):  
Sisca Indah Pratiwi ◽  
Tatik Widiharih ◽  
Arief Rachman Hakim

Based on Central Java Regional Police data, traffic accidents from 2017 to 2018 increased from 17.522 to 19.016 or 8,54 percent. To reduce the number of traffic accidents in Central Java, the initial step was carried out by grouping districts/cities that had the same accident level characteristics based on vehicle type with cluster analysis. The ward and average linkage method is a hierarchical cluster analysis method. ward method can maximize cluster homogeneity. While the average linkage method can generate clusters with small cluster variants. In this study using a measure of squared euclidean distance to measure the similarity between pairs of objects. To determine the quality of clustering results, the validation dunn index and cophenetic coefficients corelation are used. Based on the results of the clustering, the optimal number of clusters is obtained at q = 5 for the average linkage method with the results of validation dunn index = 0,08571196 and the rcoph = 0,687458. Keywords: Accidents, Cluster Analysis, Ward Method, Average linkage, Squared Euclidean Distance, Dunn Index, Cophenetic Correlation Coefficient


2017 ◽  
Vol 7 (2) ◽  
pp. 76
Author(s):  
Ferry Kondo Lembang ◽  
Patresya Yulita Lessil ◽  
Salmon Notje Aulele

Regional gross domestic product is one of the important indicators to determine economic conditions in an area. Therefore it is very interesting to discuss and to determine the economic progress of a region. Cluster anlysis aims to classify objects based on the characteristics into cluster that have the properties that are relatively similar and clearly distinguish between one cluster agains another. The main objective of the research that classifies 33 provinces based on the value of regional gross domestic product at constant price in 2013 using hierarchical cluster analysis for average linkage method. The results showed that the cluster were carried out on 33 provinces in Indonesia formed 3 cluster with details of that cluster 1 consisting of Sumatera, Kalimantan, Sulawesi, Nusa Tenggara, Bali, Papua, Maluku and Jawa Tengah, DI Yogyakarta, and Banten, cluster 2 consisting of 1 provinces of DKI Jakarta and cluster 3 which consists of 2 provinces namely Jawa Barat dan Jawa Timur.


2016 ◽  
Vol 2 ◽  
pp. 33-36 ◽  
Author(s):  
Jiban Shrestha

The determination of diversity among inbred lines is important for heterosis breeding. Sixty maize inbred lines were evaluated for their eight agro morphological traits during winter season of 2011 to analyze their genetic diversity. Clustering was done by average linkage method. The inbred lines were grouped into six clusters. Inbred lines grouped into Clusters II had taller plants with maximum number of leaves. The cluster III was characterized with shorter plants with minimum number of leaves. The inbred lines categorized into cluster V had early flowering whereas the group into cluster VI had late flowering time. The inbred lines grouped into the cluster III were characterized by higher value of anthesis silking interval (ASI) and those of cluster VI had lower value of ASI. These results showed that the inbred lines having widely divergent clusters can be utilized in hybrid breeding programme.


Author(s):  
Priscilla Ramos Carvalho ◽  
Casimiro Sepúlveda Munita ◽  
André Luiz Lapolli

The literature presents many methods for partitioning of data set, and is difficult choose which is the most suitable, since the various combinations of methods based on different measures of dissimilarity can lead to different patterns of grouping and false interpretations. Nevertheless, little effort has been expended in evaluating these methods empirically using an archaeological data set. In this way, the objective of this work is make a comparative study of the different cluster analysis methods and identify which is the most appropriate. For this, the study was carried out using a data set of 45 samples of ceramic fragments, analyzed by instrumental neutron activation analysis (INAA). The methods used for this study were: Single linkage, Complete linkage, Average linkage, Centroid and Ward. The validation was done using the cophenetic correlation coefficient and comparing these values the average linkage method obtained better results. A script of the statistical program R with some functions was created to obtain the cophenetic correlation. By means of these values was possible to choose the most appropriate method to be used in the data set.


2020 ◽  
Vol 7 (4) ◽  
pp. 225-234
Author(s):  
Miriam Andrejiova ◽  
Zuzana Kimakova

The development of the transport segment is currently an essential process which affects several other industries. The transport infrastructure and the services provided in this sector influence economic growth, the efforts aimed at increasing competitiveness, as well as prosperity of the society. One of the key problems Slovakia is facing is the long-term growth of differences between individual regions. The present article deals with the evaluation and comparison of selected transport infrastructure indicators in eight regions of Slovakia. The evaluation was carried out by applying basic statistical methods and multiple-criteria statistical methods. Every region was characterised by 20 selected variables describing its uniqueness (e.g. population, area, GDP per capita, road infrastructure etc.). The evaluation of similarities between individual regions in terms of selected variables was carried out by applying the Principal Component Analysis (PCA) and Hierarchical Cluster Analysis. Within the PCA, the original input variables were replaced with three principal components describing as much as 86.68% of the cumulative variance. The average linkage method, as one of the hierarchical methods, was applied to create a dendrogram representing the similarities between the regions of Slovakia. The cophenetic correlation coefficient value of CC=0.936 confirmed the proper selection of the average linkage method. The output of the cluster analysis was that 8 regions of Slovakia were divided into five similar homogenous clusters based on the examined variables. The final analysis indicated that the transport infrastructure and the development thereof significantly affect the differences between individual regions of Slovakia and, as a matter of fact, they belong to the factors creating such differences.


2016 ◽  
Author(s):  
Ariana Hernández ◽  
Hector S Espinosa-Pérez ◽  
Valeria Souza

The fish community in the Churince system includes endemic, native and introduced species. Fish diets were analysed in order to evaluate the tropho-dynamics of the community. Nine sampling campaigns were carried out between February 2011 and May 2014, and 556 specimens of nine fish species were collected. Stomach contents were analysed using the Index of Relative Importance (IRI) and the Index of Absolute Importance (RIa). Similar groups were defined for the trophic chain using the average linkage method. Feeding strategies were stenophagic in only the species Herichthys minckleyi and euryphagic in the other eight species. The main food categories found in the stomach contents of the fish community were insects, crustaceans, gastropods, plants and teleosts. Four functional groups were defined for the trophic chain, with no top consumer fish species. Despite this, the fish were observed to be regulators, mainly of invertebrates. The chain reaction in the control of food was thus greater from the top to the bottom.


2021 ◽  
Vol 2 (1) ◽  
pp. 16-20
Author(s):  
Fachruddin Hari Anggara Putera ◽  
Septina F. Mangitung ◽  
Madinawati ◽  
Lilies Handayani

Fisheries are one of the agricultural sub-sectors that play an important role in contributing to income figures for the state and the region because most of Indonesia's territory is water so that the fisheries sector is a sub-sector that is feasible to be developed in this country, one of which is through aquaculture. One of the efforts that can increase and maintain productivity in the aquaculture sector is to classify provinces that produce aquaculture production into groups based on the similarity of characteristics possessed by each province in Indonesia. In this study, clustering was carried out using cluster analysis using the average linkage method and based on the analysis results obtained showed that cluster 1 consists of 25 provinces, cluster 2 consists of 5 provinces, cluster 3 consists of 2 provinces, cluster 4 consists of 1 province, and cluster 5 consists of 1 province with a standard deviation value within a cluster of 11,729 and a standard deviation between clusters of 118,745.


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