Tropical Diversity (2019) 1 (1): 26-31.

ISSN: 2596-2388

DOI: 10.5281/zenodo.11098022

RESEARCH ARTICLE

26

BioCalc: a software tool for the calculation of biovolume of phytoplankton

samples

BioCalc: uma ferramenta de software para o cálculo do biovolume em amostras

fitoplanctônicas

Edinaldo Nelson dos Santos-Silva1* https://orcid.org/0000-0002-3340-4541, Raize Castro Mendes1

https://orcid.org/0000-0003-1215-7702, Mauro José Cavalcanti2 https://orcid.org/0000-0003-2389-1902

1Laboratório de Plâncton, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Av. André

Araújo, 2936, Aleixo, CEP 69060-000 Manaus, AM. E-mail: nelson@inpa.gov.br

2Ecoinformatics Studio, Caixa Postal 46521, CEP 20551-940 Rio de Janeiro, RJ

*Email: nelson@inpa.gov.br

Received: February 28, 2019 / Accepted: June 14, 2019 / Published: June 14, 2019

Resumo A estimativa do biovolume celular,

baseada em medidas de dimensões lineares da

forma, adaptadas a modelos geométricos

padronizados, é importante para o estudo da

ecologia do fitoplâncton. Contudo, cálculos

demorados são demandados para a estimativa do

biovolume a partir de medidas lineares. Neste

trabalho, uma ferramenta de software simples é

apresentada para auxiliar no cálculo do biovolume

das amostras de fitoplâncton, usando modelos

geométricos e observações microscópicas

convencionais. O software BioCalc implementa as

fórmulas mais recentes disponíveis na literatura

para calcular o biovolume celular com base em

um conjunto de 31 formas geométricas.

Palavras-Chave: biovolume, fitoplâncton,

morfometria, software.

Abstract The estimate of cell biovolume, based

on measurements of linear dimensions of shapes

adapted to standard geometric models, is

important for the study of phytoplankton ecology.

However, time-consuming calculations are

required for the estimation of biovolume from

linear measurements. In this paper, a simple, user-

friendly multiplatform software tool is presented

to aid in the calculation of the biovolume of

phytoplankton samples, using geometric models

and conventional microscopic observations. The

BioCalc software implements the most recent

formulae available in the literature for calculating

cell biovolume on the basis of a set of 31

geometric shapes.

Keywords: biovolume, phytoplankton, morphometrics,

software.

Santos-Silva et al. (2019)

BioCalc software

27

Introduction

Water covers most of the planet Earth. In

aquatic environments, phytoplanctonic algae are

the main primary producers. Currently, with the

degree of degradation of these environments, the

use of algae and several of their attributes for

monitoring or evaluating environmental quality is

increasing and justified by the advantages that

these organisms present. However, one of the

major difficulties in the use of phytoplanctonic

algae is the fact that they present an immense

diversity of shapes and sizes, which makes

interspecific comparison difficult and often

inappropriate.

Knowledge of the structure of

phytoplankton communities is of great importance

in limnological studies, in order to understand the

dynamics of these communities and their

interactions with the abiotic environment, as well

as to allow the monitoring of environmental

conditions that can be inferred from attributes like

species composition and biomass (Vadrucci et al.,

2007; Fonseca et al., 2014). Whereas species

composition require floristic inventories and

taxonomic identification, biomass can be

evaluated more directly by an estimate of the

biovolume or cell volume, based on

measurements of linear dimensions and adaptation

of shapes to standard geometric models

(Hillebrand et al., 1999; Sun & Liu 2003; Saccà

2017). So it becomes possible to make

independent comparisons of shape or size.

Perhaps the simplest and most useful way to do

this is by an estimate of the biovolume, using

linear measurements according to the geometric

shape of organisms, which can be done with a

common microscope available in all laboratories

that deal with this question. For these calculations,

there are formulae, some complex enough that

may require precious time to calculate. But this

time would be saved by taking the measurements

and automating the biovolume calculations. These

biovolume measurements can be used according

to the objectives of each study, whether from the

population, specific or general point of view of

the whole group studied.

In general lines, calculation of the

biovolume involves taking measurements of linear

dimensions (e.g. length, width, diameter, height,

etc.) from cells of each species (in μm) and the

calculation of the volume of each cell, using a

geometric formula which better represents the cell

shape and calculation of mean cell volume for the

respective species (in μm3). The biovolume (in

mm3 L-1) per taxon and sample is calculated by

multiplying the mean cell volume (in μm3) of the

taxon by the number of counted cells (cells mL-1

or cells L-1). Assuming that the phytoplankton

cells have a density equivalent to that of water (1

mm3 L-1 = 1 mg L-1), then the biovolume (in mm3

L-1) of phytoplankton cells can be converted in

wet weight (in mg L-1) or carbon content (in mgC

L-1).

Several computer programs have been

developed to aid in the calculation of the

biovolume of phytoplanktonic or bacterial

samples, using automatic or semi-automatic

methods of image analysis (Fry & Davies, 1985;

Bjørnsen, 1986; Bloem et al., 1995; Blackburn et

Santos-Silva et al. (2019)

BioCalc software

28

al., 1998; Carpentier et al., 1999; Zeder et al.,

2011). However, the most general and direct

method for calculating cell volume is based on the

morphometric approach described above, using

conventional observations from optical

microscopy (Hillebrand et al., 1999, Sun & Liu,

2003), and no software is available for performing

such calculations.

In this paper, a user-friendly computer

program is presented to aid in the calculation of

the biovolume of phytoplankton samples, using

geometric models and conventional microscopic

observations.

Materials and Methods

For implementing the calculation of

biovolume, the formulas developed by Hillebrand

et al. (1999), updated by Sun & Liu (2003), were

applied.

The software, named BioCalc, was

designed to operate as a 32-bits and 64-bits native

application, in PC-compatible microcomputers,

running under Microsoft Windows and

GNU/Linux operating systems.

The development environment adopted

was Lazarus (www.freepascal.lazarus.org), based

on the Free Pascal language and available for MS-

Windows, GNU/Linux and Mac OS operating

systems. The choice was guided by taking into

account the resources provided by this software

tool, as the easy design of graphic user interfaces,

language flexibility, efficiency and reliability of

the compiler and multiplatform rapid application

development.

Results

In its initial version, the BioCalc software

uses an intuitive interface, consisting of a simple

form with a selection list of morphotypes and

specific fields for the entry of measurements for

each morphotype (Fig. 1).

Santos-Silva et al. (2019)

BioCalc software

27

Figure 1 – Screenshot of the program for the calculation of biovolume.

For each morphotype chosen in the selection list,

the program automatically enables the respective

fields for the entry of measurements (in

micrometers) from the cell corresponding to the

selected morphotype. The “Calculate” button

allows the user to confirm the introduced data and

the volume and area are then calculated.

All the measurements entered for each

cell, as well as the calculated values of area and

volume, are stored in a text-delimited file,

automatically created and maintained by the

program during its execution. This file is a table,

where each line represents a cell and each column

corresponds to the measurements taken on each

cell, according to its morphotype, with two

additional columns corresponding to the values

calculated for area and volume of the respective

cell. The file can be opened by any electronic

spreadsheet software (Microsoft Excel,

LibreOffice Calc, etc.), for performing statistical

analyses and creating plots (Fig. 2).

Santos-Silva et al. (2019)

BioCalc software

30

Figure 2 – Data file created by the program with the results from calculation of biovolume.

Discussion

Estimates of biomass are fundamental in

studies of plankton ecology. Different methods

have been proposed with this aim, based on

geometric models or computational algorithms.

Geometric models combined with observations by

optical microscopy provide a direct and effective

approach for the calculation of cell volume of

phytoplankton samples. In this context, an

interactive and multiplatform software tool for

personal computers offers a simple alternative to

this calculation.

The development of a version for mobile

devices (tablets and cellphones running the

Android operating system) will widen the

possibilities of application of this tool, facilitating

its use in field conditions and contributing to

expedite ecological studies of plankton in the

most remote regions, as the Amazon Basin and

other tropical river basins.

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