Glossary

1 Abiotic. Not related to a living organism.

2 Abundance. The total number of a taxon or taxa individuals in an area, volume, population or community.

3 Acanthocephala. A small phylum of parasitic invertebrates that comprises the thorny-headed worms.

4 Algal bloom. A massive increase in the number of phytoplankton cells, which can be either beneficial or harmful.

5 Amphibian. A cold-blooded vertebrate animal of a class that comprises frogs, toads, newts, salamanders, and caecilians. They are distinguished for having an aquatic gill-breathing larval stage followed (typically) by a terrestrial lung-breathing adult stage.

6 Analysis of variance. A procedure based on the decomposition of the total variance of an experiment’s offset into its partial variances, for example those due to experimental treatments and those due to error; variance ratios are computed as the quotient of the variance due to each treatment times the variance due to error, and the test’s significance by contrasting this result against F distribution.

7 Anoxia. A complete lack of oxygen.

8 Benthic-organisms. Species living on the sea bottom, either attached to a substrate, free moving over it, or embedded or burrowing in it.

9 Bioavailability. The existence of a chemical element in a state that allows its assimilation by living organisms, so that its positive or negative effects can be exerted.

10 Bioavailable fraction. Refers to the metal fractions that organisms can absorb in the form that they are present in a given ecosystem.

11 Biodiversity hotspot. A threatened region with large number of species of at least 1500.

12 Bioindicators. Attributes of biological systems that are used to discern the properties of an environment. Species or species associations were firstly used as indicators but later other organization levels such as biological communities were employed, which is particularly useful for contamination studies. Indicator species are those living organisms or their remains that allow discerning the occurrence of a phenomenon or condition either at the present or in the past which is related to environmental conditions.

13 Biomass. The sum of all living organisms in a given area or at a given trophic level, usually expressed in terms of living or dry mass.

14 Biotic. Refers to the living constituents of an environment.

15 Biotoxines. Poisonous chemical compounds produced by living organisms.

16 Bird. Homeoterm egg-laying vertebrate animal distinguished by the possession of feathers, forelimbs modified into wings, a beak, and typically by being able to fly. Formerly it was grouped into class Aves, but currently into Theropoda, and considered as the only extant dinosaurs.

17 Bottom-up control. The regulation system of trophic levels in which the abundance of individuals at the higher levels is determined by the factors at the lower levels.

18Bromeliad. A plant from tropical and subtropical America, typically having short stems with rosettes of stiff, spiny leaves. Some kinds are epiphytic and many are cultivated as pot plants.

19 Canonical Correspondence Analysis (CCA). A multivariate method to elucidate the relationships between biological assemblages of species and their environment. The method is designed to extract synthetic environmental gradients from ecological data-sets. Gradients are the basis for succinctly describing and visualizing the differential habitat preferences (niches) of taxa through an ordination diagram.

20 Carbonates. Chemical compounds characterized by the (CO₃)^-2 complex. The main mineral forms are calcite and dolomite, which are the main constituents of sedimentary or metamorphic rocks.

21 Cladoceran. A minute branchiopod crustacean of the Cladocera order, which includes the water fleas.

22 Classification. In taxonomy, the arrangement of organisms into a nomenclatural hierarchy, according to their degree of evolutionary relatedness.

23 Coastal lagoon. A coastal water body, found on all continents, usually with its main axis oriented parallel to the coastline, and separated from the ocean by a barrier, connected to the sea by one or more inlets which remain open at least intermittently, so that a mixture of seawater and sea biota with coastal or freshwater occurs. They are typically shallow.

24 Coliforms. Gram-negative, non-sporulated bacilli able to ferment lactose with gas production, considered as indicators of fecal pollution.

25 Total. Ferment lactose with gas production at 37°C.

26 Fecal. Fermenting lactose with gas production when incubated at a temperature of 44.5°C.

27 Colony Forming Units (CFU). The number of bacterial cells present that can grow in a culture medium under the incubation conditions employed. Each colony on a Petri dish in principle is formed from a single growing bacterial cell; thereby counting the colonies allows estimating the number of CFUs in a sample.

28 Copepod. A small or microscopic aquatic crustacean of the large class Copepoda.

29Community. An integrated group of species inhabiting a given area; the organisms within a community influence one another’s distribution, abundance, and evolution.

30 Crustacean. An arthropod of the mainly aquatic subphylum Crustacea, which comprises macroscopic forms such as crabs, lobsters, shrimp, krill or barnacles, but also microscopic forms such as copepods and water fleas.

31 Data matrix. A table where each row represents a variable or system descriptor and each column a state (a point in time or space) of the system.

32 Decapod. A crustacean of the order Decapoda, such as a shrimp, crab, or lobster.

33 Dendrogram. The graphical representation of a cluster analysis where hierarchical branching is observed. The usual convention is that two objects or entities are most similar when the link among them occurs nearer to the plot’s base.

34 Denitrification. Is a microbe-facilitated process of nitrate reduction performed by a large group of heterotrophic facultative anaerobic bacteria, that may ultimately produce molecular nitrogen (N₂) through a series of intermediate gaseous nitrogen oxide products. This respiratory process reduces oxidized forms of nitrogen in response to the oxidation of an electron donor such as organic matter.

35 Detritus. Organic matter lost from any trophic level by causes different from predation or grazing, in diverse stages of decay, along with associated biota, and usually fine-grained inorganic components such as silt or clay.

36 Diatoms. Division Bacillariophyta Hustedt. Unicellular microalgae, including both solitaire and colonial forms. Their cells are enclosed within a silica-impregnated cell wall forming two valves and several cingular or connective bands, known as frustula.

37 Dinoflagellates. Division Pyrrophyta. Mainly planktonic microorganisms moving through water by means of two unequal undilopodia and presenting orange-red pigments. Several among them present photosynthetizing chromatophores in the protoplast and cellulose in their cell wall, and are thus similar to plants. There are also heterotrophic forms that resemble animals because of their locomotive abilities. Most of them present a special type of nucleus with fibrillar chromosomes that remain loosely condensed and visible along all the mitotic cycle.

38Direct count. It is an estimation of bacterial numbers in a sample based on cell counts from slides stained with the fluorochrome DAPI and observed under an epifluorescence microscope.

39 Distribution. This term refers to the patterns governing the spatial position of the individuals from a population across an area or territory.

40 Diversity. It relates to the absolute number of species in an assemblage, community or sample (species richness), but is also dependent on the way that organism numbers are distributed along the different species (eveness).

41 Dominance. The extent to which a given species predominates in a community because of its size, abundance or coverage, and affects the fitness of associated species.

42 Eigenanalysis. A linear algebra technique for the extraction of latent roots and vectors (eigenvalues and eigenvectors) from a square matrix; these describe matrix properties in a decreasing order as related to system variance. It is the basis for multivariate ordination methods such as principal component analysis, factor analysis and canonical correspondence analysis, among others.

43 Enteropathogenic. Microorganisms with the ability to produce gastrointestinal disease through growth-related causes and their intestinal cells invasion or destruction.

44 Enterotoxic. Microorganisms that produce toxins that can harm the gastrointestinal tract or induce systemic effects.

45 Epiphyte. A plant that grows on another plant, especially one that is not parasitic, such as the numerous ferns, bromeliads, air plants, and orchids growing on tree trunks in tropical rainforests.

46 Euclidean distance. A dissimilarity measure (distance) between two elements from a data matrix; it is the extension of Pythagoras’ Theorem to a n–dimensional space.

47 Eutrophication. The increase of biological production of an aquatic system that originates from a higher availability of nutrient salts. Even though this might appear to be a beneficial process, generally it relates with the proliferation of few primary producer species implying a decrease in species diversity. Other associated effects include oxygen depletion during the night, liberation of toxins by proliferating species, an increase in the sedimentation rate and the acquisition of unpleasant flavors or odors by water; it is thus considered as an undesirable condition.

48 Fern. A flowerless tracheophyte which has feathery or leafy fronds and reproduces through spores released from the undersides of the fronds.

49 Fish. Finned poikilotherm vertebrate animal of the classes Agnatha, Chondrichthyes or Osteichthyes, provided with gills during its whole life story, and living wholly in water. FPAS (Folin Phenol Active Substances). Compounds that react to Folin phenol, mainly tanins and lignins.

50 Function. Role of organisms within ecosystems.

51 Gram stain. It is based on the ability to allow the passage of Gram stain (crystal violet) into the bacterial cell. When it does, the cell is stained violet (Gram-positive); if not, the cell is stained red, the color of safranin, the contrast stain (Gram-negative). This character depends on the structure of the bacterial cell wall.

52 Gross primary productivity. Total carbon fixation rate without subtracting respiration. Habitat. The locality, site and particular type of local environment occupied by an organism.

53 Holoplankton. Organisms which remain as plankton throughout their entire life cycle, e.g. algae.

54 Insect. A small arthropod animal of class Insecta, that has six legs as an adult, and generally one or two pairs of wings.

55 Interstitial water. The water held in pore spaces in rock, soil or sediment.

56 Introduced species. Species that are not native to an area but brought in through human activities.

57 Jaccard index. Also known as the Jaccard similarity coefficient, is a statistic used for comparing similarity and diversity of sample sets. The Jaccard coefficient measures similarity between finite sample sets.

58Land use. Also known as land-cover change is a general term for the human modification of Earth’s terrestrial surface.

59 Leaf extract. Substances diluted in water obtained from decomposition of mangrove leaves.

60 Leaf litter. Leaves settling on the lagoon’s bottom from mangrove, as a result of their natural falling.

61 Legume. A leguminous plant (member of the pea family), especially those grown as a crop.

62 Liana. An either herbaceous or woody climbing plant that hangs from trees, but is permanently rooted to soil, especially abundant and diverse in tropical rainforests, but which are also found in colder and drier environments.

63 Macroalgae. Commonly termed “seaweeds”, are multicellular, macroscopic benthic algae belonging to green (phylum Chlorophyta), red (phylum Rhodophyta), and brown (phylum Phaeophyta) taxonomic groups. They are found in estuaries throughout the world, attached to substrates or drifting in the water column.

64 Mangroves. Dicotyledonous woody trees and shrubs that grow above mean sea level to form intertidal forests along subtropical and tropical coasts (Alongi, 2016).

65 Mangrove forest. Coastal wetland vegetation dominated by tree species tolerant to some degree of salinity.

66 Marine pollution. The human-related introduction of matter or energy, both directly or indirectly, into the environment that generate noxious effects implying a hazard for living beings or human health, handicapping productive marine activities.

67 Marsupial. A mammal of Infraclass Marsupialia whose members are born incompletely developed and are typically carried and suckled in a pouch at the mother’s belly. Marsupials are found chiefly in Australia, New Guinea and America.

68 Metalloid. Elements that have characteristics between metals and non-metals.

69Metals. Elements able to conduct heat and electricity, which have a characteristically shiny appearance. In their native state they are solid, except for mercury (Hg) that regularly is liquid at room temperature.

70 Misidentification. Incorrect assignment of a specimen to a taxon.

71 Mollusk. An invertebrate of phylum Mollusca, which includes snails, slugs, mussels, and octopuses. They have a soft unsegmented body and live in aquatic or damp habitats; most kinds have an external calcareous shell.

72 Most Probable Number (MPN). Estimated number of active cells in a sample or culture, based on the probability of certain combination of positive and negative results (for example bacterial growth) in different sample dilutions. This is obtained from the Poisson statistical distribution, and generally is shown in MPN tables for different combinations of positive results at various dilutions.

73 Mutagenic. A chemical or physical agent that changes the genetic material of an organism, usually DNA, thus increasing the frequency of mutations above the natural background level.

74 Natural services. Tangible or intangible benefits that ecosystems provide to humans.

75 NDVI. Normalized Difference Vegetation Index. The most common method to measure and map the density of green vegetation over the Earth using satellite remote sensors.

76 Nematode. A worm of the large phylum Nematoda, such as a roundworm or thread-worm.

77 Nitric oxide. A free Nitrogen-Oxygen chemical radical produced through the bacterial denitrification process.

78 Nitrogen fixation. Is a process by which atmospheric nitrogen (N₂) is converted into ammonia (NH₃) in the presence of nitrogenase. The fixation process frees nitrogen atoms from their triply bonded diatomic form, N≡N, to be used in other ways.

79 Nitrogenases. The enzymes responsible for the nitrogen (N₂) reduction to ammonia (NH₃). Nitrogenases are the only family of enzymes known to catalyze this reaction, which is a key step in the process of nitrogen fixation. They are only found naturally in certain microorganisms such as the symbiotic Rhizobium and Frankia, or the free-living Azospirillum and Azotobacter.

80 Nitrous oxide. Nitrous oxide (N₂O) accounts for about 5.9 % of all U.S. greenhouse gas emissions from human activities. Nitrous oxide is naturally present in the atmosphere as part of the Earth’s nitrogen cycle, and has a variety of natural sources. However, human activities such as agriculture, fossil fuel combustion, wastewater management, and industrial processes are increasing the amount of N₂O in the atmosphere. Nitrous oxide molecules stay in the atmosphere for an average of 114 years before being removed to a sink or destroyed through chemical reactions. The impact of 1 pound of N₂O on warming the atmosphere is almost 300 times that of 1 pound of carbon dioxide.

81 Nonparametric methods for the species richness estimation. Methods and estimators concerned with the problem of predicting the number of new species that will be discovered in an additional survey given that an initial survey has already been conducted. These are termed nonparametric because they are not based on the parameter of a species abundance model.

82 Nortes. Climatic season characterized by strong winds coming from the North to the Gulf of Mexico, commonly occurring from October to March.

83 Odonate. A predatory insect of the order Odonata; a dragonfly or damselfly.

84 Orchid. A plant with complex flowers that are often showy or bizarrely shaped, having a large specialized lip (labellum) and frequently a spur. Orchids occur worldwide, especially as epiphytes in tropical forests, and are valuable hothouse plants.

85 Ordering. Deploying (to plot) a cloud of data points in a two or three-dimensional coordinate system, to make visible the relationships between data points in a multidimensional space. It is also the order of a points set with respect to one or more axes.

86 Organic matter. In soils or sediments, it is the product of the chemical decomposition of organisms and classified in humic (generally refractory) and not humic (generally labile) compounds.

87 Orthorectification. Process of removing the effects of image perspective (tilt) and relief (terrain) effects for the purpose of creating a planimetrically correct image. The resultant orthorectified image has a constant scale and so the features are represented in their ‘true’ positions. This allows for the accurate direct measurement of distances, angles, and areas (i.e. mensuration).

88 Otter. A semiaquatic fish-eating mammal of the weasel family, with an elongated body, dense fur, and webbed feet.

89 Pentastomid. Any of numerous parasitic wormlike animals of the crustacean class Pentastomida (often regarded as a distinct phylum or subphylum), which infest the lungs and nasal passages of vertebrates.

90 Phylogeny. The evolutionary development of an organism or group of organisms in time, as distinguished from ontogeny, which is the development of an individual from fertilization of the egg until adulthood.

91 Phytoplankton. A community of microscopic organisms of relatively simple shapes, mostly living by photosynthesizing and suspended in the water column.

92 Platyhelminthes. A phylum of invertebrates that comprises flatworms.

93 Predation. The killing and eating of other animals.

94 Primary production. Mainly based on the biochemical process of photosynthesis, in which solar energy is biochemically fixed. Primary producers in the aquatic environment are macrophytes, phytoplankton and phytobenthos.

95 Primary productivity. It is the rate at which energy is stored in the organic matter of autotrophs through photosynthesis.

96 Principal component analysis. It is based on the rigid rotation of coordinate axes (without deforming) so that the variability and structure of the data point cloud can be represented as a bi- or tridimensional plot.

97 Productivity. The rate at which something is produced. It is also the quotient of the organic matter produced at a trophic level times the biomass from which it was produced.

98 Red tide. A natural phenomenon caused by the numerical increase of one or several microalgae in water, which because of its concentration gives a characteristic coloration to the water, however some may be colorless.

99Remote sensing. Is a way of collecting and analyzing data to get information about an object without the instrument being in direct contact with the object.

100 Reptile. Poikiloterm vertebrate animal of a class that includes snakes, lizards, crocodiles, turtles, and tortoises. They are distinguished by having a dry scaly skin, for being devoid of external gills during their whole life history, and typically laying soft-shelled eggs on land.

101 Rhizocephalan. A parasitic crustacean of the order Rhizocephala.

102 Rotifer. A microscopic multicellular aquatic animal of the phylum Rotifera.

103 Rotifera. A phylum of microscopic suspensivorous metazoans (multicellular organisms). About 2030 species are known and are classified into three main groups: Seisonida of only 3 known marine species, Monogononta with 1570 species and Bdelloidea with 461. They are organisms of a size between 50 to 2.000 μm. They are composed approximately by 1000 cells and filter small food particles from the water column by a ciliated crown located in the front portion of the body. The crown also can be used for locomotion, however some species are sessile.

104 Seagrass. A grass-like monocotyledonous plant that lives in or close to the sea.

105 Secchi disk. A metal or plastic disc 0.3 m in diameter, white or with white and black alternating quadrants, used to estimate the depth of effective penetration of sunlight into the water, based on the point where the observer loses sight of it.

106 Sediment. Particulate matter that has been transported by wind, water or ice and subsequently deposited, or that has been precipitated and settled from water; sedimentation. Soluble reactive phosphorus. Filterable portion of inorganic phosphorus stable in solution and that is easily assimilated by the primary producers.

107 Species accumulation curves. A ‘species accumulation curve’, or ‘collector’s curve’, is a plot of the cumulative number of species discovered S (n), within a defined area, as a function of some measure n of the effort expended to find them.

108 Species richness. Species richness refers to the number of species in a given area; the more species, the greater the species richness.

109Spectral Signature. Is the wavelength composition of radiation reflected as a function of wavelength-specific absorption and reflection by some surface.

110 Synonymy. According to the ‘International Code of Zoological Nomenclature’, a chronological list of all scientific names that have been applied, correctly or incorrectly, to a given taxon.

111 Systematics. The study of the historical evolutionary and genetic relationship between organisms and their phenotypic similarities and differences.

112 Tanaidacea. A small order of malacostracan crustaceans (division Peracarida) often included in the Isopoda and intermediate in character between that order and the Cumacea. Taxa. Plural of taxon.

113 Taxon. A grouping in a scientific classification of organisms, e.g. a family, genus or species.

114 Top-down control. The regulation system of trophic levels by which the abundance of herbivores in the lower trophic levels is determined by factors from the higher levels.

115 Trematod. A parasitic flatworm of the class Trematoda.

116 Trophic cascade. The effect of size changes of a given population on lower non-consecutive components of the food web.

117 Trophic level. A level in a food web.

118 Treatments. Any factor for which its effects are to be measured in an experimental design.

119 UPGMA. Abbreviation of Unweighted Pair-Group Method with Arithmetic mean. It is a simple agglomerative (bottom-up) hierarchical clustering method.

120 Valid name. According to the ‘International Code of Zoological Nomenclature’, the correct scientific name for a taxon.

121Viable count. The estimation of bacterial numbers in a sample by counting the Colony Forming Units (CFU) on an agar plate inoculated with a known dilution of the sample.

122 Zoogeographical province. A bio geographical unit that is distinguished by a fauna which is more or less distinctive at the species, genus, family, or order level. Areas with at least 10 % endemic species are considered provinces.

123 Zooplankton. Microscopic animals that live and drift in water.